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ReactionMechanismGenerator / RMG-Java

The Java version of RMG: Reaction Mechanism Generator
http://rmg.sourceforge.net/
MIT License
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NullPointerException error on Windows for the 1-3 hexadiene example #47

Closed athlonshi closed 14 years ago

athlonshi commented 14 years ago

On commit 165e221bcc1e07195d2ca12a7145e0a25a188c2c (the latest one I believe) The same example runs fine on Mount, but it takes 13 hours. On Windows, it encountered "NullPointerException", message as below java.lang.NullPointerException at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:315) at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544) at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1416) at RMG.main(RMG.java:57) Troublesome FAME input saved to ./fame/405_input.txt Troublesome FAME result saved to ./fame/405_output.txt Falling back to modified strong collision mode for this network.

rwest commented 14 years ago

Has this been fixed yet? We just had a slew of commits trying to address NullPointerException errors.

athlonshi commented 14 years ago

No, I tried yesterday's new commit, but the problem is the same.

athlonshi commented 14 years ago

I should make it clear. The fix helps to solve the issue on Monch as the example case was finished successfully within 5 hours. But on Windows, I still see the nullpointer error.

athlonshi commented 14 years ago

Standard example, run in netbeans:

PDepNetwork #256 (C7H12JJ): 0 included and 1 nonincluded net reactions.
PDepNetwork #257 (C7H12JJ): 0 included and 1 nonincluded net reactions.
PDepNetwork #258 (C11H16JJ): 0 included and 1 nonincluded net reactions.
fitted Er < 0: -1.543800359977034
SPC(330)=C6H9J(15)+C5H7J(13)
PDepNetwork #259 (C11H16JJ): 0 included and 1 nonincluded net reactions.
fitted Er < 0: -14.93245276007422
SPC(331)=C6H9J(15)+C5H7J(13)
PDepNetwork #260 (C11H16JJ): 0 included and 1 nonincluded net reactions.
fitted Er < 0: -1.7437801916070654
SPC(332)=C6H9J(15)+C5H7J(13)
null
Troublesome FAME input saved to ./fame/261_input.txt
java.lang.NullPointerException
Troublesome FAME result saved to ./fame/261_output.txt
Falling back to modified strong collision mode for this network.
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1416)
        at RMG.main(RMG.java:57)
null
Troublesome FAME input saved to ./fame/261_input.txt
Troublesome FAME result saved to ./fame/261_output.txt
Error running FAME.
java.lang.NullPointerException
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:415)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1416)
        at RMG.main(RMG.java:57)
BUILD SUCCESSFUL (total time: 7 minutes 6 seconds)

Fame log:

Reading network information...
 Method set to modified strong collision
 Temperatures = 302.4700477907563 323.1454251046035 369.86016925606674 455.98707366821293 609.6487731779273 885.262196646079 1353.6353685312504 1896.7383303620059
 Pressures = 1252.8150658894924 6674.665337780328 99999.99999999997 1498202.4556942817 7982024.061069267
 Model set to Chebyshev
 Number of grains = 251
 dEdown = 6556.646918661306 J/mol
 Found 3 species
     Species 1 is c11h16jj(332)                                                                                                                   
     Species 2 is c6h9j(15)                                                                                                                       
     Species 3 is c5h7j(13)                                                                                                                       
 Found 1 isomers
 Found 1 reactants
 Found 0 products
     Isomer 1 is 1
     Isomer 2 is 2 and 3
 Found 1 path reactions
     Reaction 1 is c11h16jj(332)                                                                                                                                                                                                                                                   
Zeroing lowest energy isomer...
Determining energy grains...
gmagoon commented 14 years ago

athlonshi encountered the following error with the latest version

java.lang.NullPointerException
null
Troublesome FAME input saved to ./fame/94_input.txt
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
Troublesome FAME result saved to ./fame/94_output.txt
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
Falling back to modified strong collision mode for this network.
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
null
java.lang.NullPointerException
Troublesome FAME input saved to ./fame/94_input.txt
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
Troublesome FAME result saved to ./fame/94_output.txt
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:415)
Error running FAME.
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
BUILD SUCCESSFUL (total time: 4 minutes 9 seconds)

On my system (32-bit Windows), as of 9749e2f68cd176917ea365311135a0e9307955c2, it seems to be running without error for at least 15 minutes without error. Two others report that they have run without error for over 30 minutes.

gmagoon commented 14 years ago

OK, I just loosened the error tolerance to 0.5 and I get the following after about 15 minutes:

PDepNetwork #275 (C11H15J): 0 included and 1 nonincluded net reactions.
PDepNetwork #276 (C11H15J): 0 included and 1 nonincluded net reactions.
PDepNetwork #277 (C11H15J): 0 included and 1 nonincluded net reactions.
PDepNetwork #278 (C6H9J): 0 included and 1 nonincluded net reactions.
PDepNetwork #279 (C6H9J): 0 included and 1 nonincluded net reactions.
PDepNetwork #280 (C11H13J): 0 included and 1 nonincluded net reactions.
PDepNetwork #281 (C11H13J): 0 included and 1 nonincluded net reactions.
PDepNetwork #282 (C11H13J): 0 included and 1 nonincluded net reactions.
null
java.lang.NullPointerException
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
Troublesome FAME input saved to ./fame/283_input.txt
Troublesome FAME result saved to ./fame/283_output.txt
Falling back to modified strong collision mode for this network.
PDepNetwork #283 (C12H17J): 0 included and 1 nonincluded net reactions.
java.lang.NullPointerException
null
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
Troublesome FAME input saved to ./fame/284_input.txt
Troublesome FAME result saved to ./fame/284_output.txt
Falling back to modified strong collision mode for this network.
java.lang.NullPointerException
null
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:415)
Troublesome FAME input saved to ./fame/284_input.txt
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
Troublesome FAME result saved to ./fame/284_output.txt
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
Error running FAME.
        at RMG.main(RMG.java:57)
BUILD SUCCESSFUL (total time: 16 minutes 14 seconds)
gmagoon commented 14 years ago

The two input files (283 and 284) seem to run correctly when calling FAME from command line: e.g. "%RMG%/bin/fame.exe < 284_input.txt"

rwest commented 14 years ago

remember that if the fame fails twice (RS and MSC) it writes the input and result to the same files both times, so you don't get to see the first version. It looks like 283 succeeded the second time?

athlonshi commented 14 years ago

I rerun the case and ended up with different crash point. Last time was 93 and now is 130.

Yu

jwallen commented 14 years ago

Hm...When I run the hexadiene job with the looser tolerance (0.5) on my 32-bit Windows XP partition it completes successfully (42 reactions and 13 species in the core, 1239 reactions and 504 species in the edge) in ~12 min. 445 PDepNetworks were created along the way.

Also, I don't think the number assigned to each PDepNetwork is guaranteed to be the same between runs, so you should also at least check the isomer type as well when comparing across jobs. That said, usually the numbers are fairly close, especially in the early going.

gmagoon commented 14 years ago

I reran again and it failed in about the same spot with a slightly different error message:

PDepNetwork #281 (C11H13J): 0 included and 1 nonincluded net reactions.
PDepNetwork #282 (C11H13J): 0 included and 1 nonincluded net reactions.
java.lang.NullPointerException
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
null
Troublesome FAME input saved to ./fame/283_input.txt
Troublesome FAME result saved to ./fame/283_output.txt
Falling back to modified strong collision mode for this network.
java.lang.NullPointerException
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:317)
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:415)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
null
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(Troublesome FAME input saved to ./fame/283_input.txt
RMG.java:57)
Troublesome FAME result saved to ./fame/283_output.txt
Error running FAME.
BUILD SUCCESSFUL (total time: 15 minutes 56 seconds)

Again, 283 seems to work fine from command prompt.

rwest commented 14 years ago

Seems reminiscent of b44110a4eaed1998619f9154d74ededed5d8335a

jwallen commented 14 years ago

We are trying to manipulate the g95 compiler flags to see if that will help us diagnose what is going on. In particular, we've added -Wall -fbounds-check. I also noticed that fame has the -O3 flag on (for really large optimization) and recall having some trouble with this a while back.

Edit: DASSL doesn't seem to like -fbounds-check, so I'm not using the new flags for it.

athlonshi commented 14 years ago

I was trying g95 -O2 -Wall -fbounds-check but didn't help Yu

gmagoon commented 14 years ago

Yu, what do you get if you type "java -version" at command prompt?

athlonshi commented 14 years ago

java version "1.6.0_18" Java(TM) SE Runtime Environment (build 1.6.0_18-b07) Java HotSpot(TM) Client VM (build 16.0-b13, mixed mode, sharing)

This is my JAVA version information

jwallen commented 14 years ago

Playing with compiler flags doesn't seem to help (or hurt) any, except for DASSL. Even removing -O3 from fame didn't work for Greg.

A summary of our current status as I understand it:

Windows XP 32-bit: OK (Mike, Josh) Windows Vista 32-bit: FAIL (Greg) Windows Vista 64-bit: OK (Amrit) Windows 7 32-bit: FAIL (Yu)

athlonshi commented 14 years ago

Mine is Windows7 32 bit

gmagoon commented 14 years ago

output of standard error:

PDepNetwork #281 (C11H13J): 0 included and 1 nonincluded net reactions.
PDepNetwork #282 (C11H13J): 0 included and 1 nonincluded net reactions.
Stderr:
Exception: Access Violation
At line 310 of file network.f90
Traceback: not available, compile with -ftrace=frame or -ftrace=full
FAME output file is empty; FAME job was likely unsuccessful.
jing.rxn.PDepException: FAME output file is empty; FAME job was likely unsuccessful.
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:325)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
Troublesome FAME input saved to ./fame/283_input.txt
Troublesome FAME result saved to ./fame/283_output.txt
Falling back to modified strong collision mode for this network.
PDepNetwork #283 (C12H17J): 0 included and 1 nonincluded net reactions.
PDepNetwork #284 (C12H17J): 0 included and 1 nonincluded net reactions.
PDepNetwork #285 (C12H17J): 0 included and 1 nonincluded net reactions.
Stderr:
Exception: Access Violation
jing.rxn.PDepException: FAME output file is empty; FAME job was likely unsuccessful.
At line 310 of file network.f90
Traceback: not available, compile with -ftrace=frame or -ftrace=full
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:325)
FAME output file is empty; FAME job was likely unsuccessful.
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
Troublesome FAME input saved to ./fame/286_input.txt
Troublesome FAME result saved to ./fame/286_output.txt
Falling back to modified strong collision mode for this network.
Stderr:
Exception: Access Violation
At line 310 of file network.f90
Traceback: not available, compile with -ftrace=frame or -ftrace=full
FAME output file is empty; FAME job was likely unsuccessful.
jing.rxn.PDepException: FAME output file is empty; FAME job was likely unsuccessful.
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:325)
Troublesome FAME input saved to ./fame/286_input.txt
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:424)
Troublesome FAME result saved to ./fame/286_output.txt
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
Error running FAME.
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1427)
        at RMG.main(RMG.java:57)
BUILD SUCCESSFUL (total time: 17 minutes 46 seconds)

283_input.txt:

# Collisional transfer probability model
#   Option 1: Single exponential down
#       Option must also be accompanied by unit and value of the parameter
#       Allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#       Example: SingleExpDown kJ/mol 7.14
SingleExpDown J/mol 6556.646918661306

# Bath gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 26.74026329165396
m 3.687872013825353E-10
J 1.3364709276202094E-21

# The number of species in the network (minimum of 2)
3

# Species identifier (128 characters or less, no spaces)
C12H17J(372)
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 252696.7389275495
# Thermodynamics data:
#   Standard enthalpy of formation; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#   Standard entropy of formation; allowed units are permutations of energy (J, kJ, cal, or kcal) and temperature (K, C, F, or R)
#   Heat capacity at 300, 400, 500, 600, 800, 1000, and 1500 K
J/mol 252696.7389275495
J/mol*K 547.3505984437677
7 J/mol*K
231.166
297.9008
353.21328
397.2708
463.75456
511.66135999999995
586.88968
# Species gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 161.0
m 7.812682348693461E-10
J 5.701788712858333E-21
# Harmonic oscillators; allowed units are Hz and cm^-1
74 cm^-1
2750.0
2800.0
2850.0
1350.0
1500.0
750.0
1050.0
1375.0
2950.0
3100.0
1380.0
975.0
1025.0
2750.0
2850.0
1437.5
1250.0
1305.0
750.0
350.0
2995.0
3000.0
3005.0
3010.0
3015.0
3020.0
3025.0
975.0
979.1666666666666
983.3333333333333
987.4999999999999
991.6666666666665
995.8333333333331
999.9999999999998
1300.0
1312.5
1325.0
1337.5
1350.0
1362.5
1375.0
400.0
416.6666666666667
433.33333333333337
450.00000000000006
466.66666666666674
483.3333333333334
500.0000000000001
1630.0
1638.3333333333333
1646.6666666666665
1654.9999999999998
1663.333333333333
1671.6666666666663
1679.9999999999995
1380.0
1390.0
370.0
380.0
2900.0
435.0
3000.0
3100.0
440.0
815.0
1455.0
312.49110406896443
312.49110406896443
312.49110406896443
312.49110406896443
312.49110406896443
312.49110406896443
312.49110406896443
312.49110406896443
# Rigid rotors; allowed units are Hz and cm^-1
0 cm^-1
# Hindered rotor frequencies and barriers
7 cm^-1
50.0
50.0
50.0
300.0
300.0
300.0
300.0
7 cm^-1
10.0
10.0
10.0
10000.0
10000.0
10000.0
10000.0
# Symmetry number
6

# Species identifier (128 characters or less, no spaces)
C6H8(264)
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 165820.32182800144
# Thermodynamics data:
#   Standard enthalpy of formation; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#   Standard entropy of formation; allowed units are permutations of energy (J, kJ, cal, or kcal) and temperature (K, C, F, or R)
#   Heat capacity at 300, 400, 500, 600, 800, 1000, and 1500 K
J/mol 165820.32182800144
J/mol*K 331.96400557596087
7 J/mol*K
117.31936
150.12192000000002
175.81168
195.30912
224.01136000000002
244.764
277.39920000000006
# Species gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 80.0
m 5.865010633325628E-10
J 4.989907384649363E-21
# Harmonic oscillators; allowed units are Hz and cm^-1
34 cm^-1
2950.0
3000.0
3050.0
3100.0
1330.0
1430.0
900.0
1050.0
1000.0
1050.0
2995.0
3005.0
3015.0
3025.0
975.0
983.3333333333334
991.6666666666667
1000.0000000000001
1300.0
1325.0
1350.0
1375.0
400.0
433.3333333333333
466.66666666666663
499.99999999999994
1630.0
1646.6666666666667
1663.3333333333335
1680.0000000000002
180.78761624296342
180.78761624296342
180.78761624296342
180.78761624296342
# Rigid rotors; allowed units are Hz and cm^-1
0 cm^-1
# Hindered rotor frequencies and barriers
2 cm^-1
180.0
150.0
2 cm^-1
1709.1637970718484
10000.0
# Symmetry number
2

# Species identifier (128 characters or less, no spaces)
C6H9J(15)
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 159963.26130550657
# Thermodynamics data:
#   Standard enthalpy of formation; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#   Standard entropy of formation; allowed units are permutations of energy (J, kJ, cal, or kcal) and temperature (K, C, F, or R)
#   Heat capacity at 300, 400, 500, 600, 800, 1000, and 1500 K
J/mol 159963.26130550657
J/mol*K 353.078601800321
7 J/mol*K
116.27336000000003
148.36464
175.47696000000002
198.44712
233.21616000000006
259.07328
300.66223999999994
# Species gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 81.0
m 5.932967927172225E-10
J 5.0368332472871756E-21
# Harmonic oscillators; allowed units are Hz and cm^-1
36 cm^-1
2750.0
2800.0
2850.0
1350.0
1500.0
750.0
1050.0
1375.0
2995.0
3005.0
3015.0
3025.0
975.0
983.3333333333334
991.6666666666667
1000.0000000000001
1300.0
1325.0
1350.0
1375.0
400.0
433.3333333333333
466.66666666666663
499.99999999999994
1630.0
1646.6666666666667
1663.3333333333335
1680.0000000000002
3000.0
3100.0
440.0
815.0
1455.0
663.3481775698752
662.8607117857006
664.3028673161527
# Rigid rotors; allowed units are Hz and cm^-1
0 cm^-1
# Hindered rotor frequencies and barriers
3 cm^-1
50.0
300.0
300.0
3 cm^-1
1294.687714644968
7267.850355601379
7267.850355601379
# Symmetry number
6

# The number of isomers in the network (minimum of 2)
1
# The number of reactant channels in the network
1
# The number of product channels in the network
0

# The number and identifiers of each species in the isomer
1 C12H17J(372)

# The number and identifiers of each species in the isomer
2 C6H8(264) C6H9J(15)

# The number of reactions in the network (minimum of 2)
1

# The reaction equation, in the form A + B --> C + D
C12H17J(372) (included =false) <=> C6H8(264) + C6H9J(15) (included =true)
# Indices of the reactant and product isomers, starting with 1
1 2
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 384359.8626640859
# High-pressure-limit kinetics model k(T):
#   Option 1: Arrhenius
#   Arrhenius preexponential factor; allowed units are combinations of volume {m^3, L, or cm^3} and time {s^-1}
#   Arrhenius activation energy; allowed units are J/mol, kJ/mol, cal/mol, or kcal/mol
#   Arrhenius temperature exponent
Arrhenius
s^-1 3.0340175410042606E14
J/mol 131663.1237365364
0.0

286_input.txt:

################################################################################
#
#   FAME input file
#
################################################################################

# All syntax in this file is case-insensitive

# The method to use to extract the phenomenological rate coefficients k(T, P)
#   Options: ModifiedStrongCollision, ReservoirState
ModifiedStrongCollision

# The temperatures at which to estimate k(T, P)
#   First item is the number of temperatures 
#   Second item is the units; options are K, C, F, or R
#   Remaining items are the temperature values in the specified units
8 K
302.4700477907563
323.1454251046035
369.86016925606674
455.98707366821293
609.6487731779273
885.262196646079
1353.6353685312504
1896.7383303620059

# The pressures at which to estimate k(T, P)
#   First item is the number of pressures 
#   Second item is the units; options are bar, atm, Pa, or torr
#   Remaining items are the temperature values in the specified units
5 Pa
1252.8150658894924
6674.665337780328
99999.99999999997
1498202.4556942817
7982024.061069267

# The interpolation model to use to fit k(T, P)
#   Option 1: No interpolation
#       Example: None
#   Option 2: Chebyshev polynomials
#       Option must be accompanied by two numbers, indicating the number of
#       terms in the Chebyshev polynomials for temperature and pressure, 
#       respectively
#       Example: Chebyshev 4 4
#   Option 3: Pressure-dependent Arrhenius
#       Example: PDepArrhenius
Chebyshev 4 4

# A method for determining the number of energy grains to use
#   Option 1: Specifying the number to use directly
#       Example: NumGrains 201
#   Option 2: Specifying the grain size in J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#       Example: GrainSize J/mol 4.184
NumGrains 251

# Collisional transfer probability model
#   Option 1: Single exponential down
#       Option must also be accompanied by unit and value of the parameter
#       Allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#       Example: SingleExpDown kJ/mol 7.14
SingleExpDown J/mol 6556.646918661306

# Bath gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 26.74026329165396
m 3.687872013825353E-10
J 1.3364709276202094E-21

# The number of species in the network (minimum of 2)
3

# Species identifier (128 characters or less, no spaces)
C12H17J(375)
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 269430.3189854747
# Thermodynamics data:
#   Standard enthalpy of formation; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#   Standard entropy of formation; allowed units are permutations of energy (J, kJ, cal, or kcal) and temperature (K, C, F, or R)
#   Heat capacity at 300, 400, 500, 600, 800, 1000, and 1500 K
J/mol 269430.3189854747
J/mol*K 555.0459149051496
7 J/mol*K
233.34168
294.17704000000003
346.72808000000003
390.7856
457.8551200000001
507.10080000000005
583.70984
# Species gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 161.0
m 7.812682348693461E-10
J 5.701788712858333E-21
# Harmonic oscillators; allowed units are Hz and cm^-1
74 cm^-1
2750.0
2800.0
2850.0
1350.0
1500.0
750.0
1050.0
1375.0
2950.0
3100.0
1380.0
975.0
1025.0
2750.0
2850.0
1437.5
1250.0
1305.0
750.0
350.0
2995.0
3000.0
3005.0
3010.0
3015.0
3020.0
3025.0
975.0
979.1666666666666
983.3333333333333
987.4999999999999
991.6666666666665
995.8333333333331
999.9999999999998
1300.0
1312.5
1325.0
1337.5
1350.0
1362.5
1375.0
400.0
416.6666666666667
433.33333333333337
450.00000000000006
466.66666666666674
483.3333333333334
500.0000000000001
1630.0
1638.3333333333333
1646.6666666666665
1654.9999999999998
1663.333333333333
1671.6666666666663
1679.9999999999995
1380.0
1390.0
370.0
380.0
2900.0
435.0
3000.0
3100.0
440.0
815.0
1455.0
672.938986520273
672.938986520273
672.938986520273
672.938986520273
672.938986520273
672.938986520273
672.938986520273
672.938986520273
# Rigid rotors; allowed units are Hz and cm^-1
0 cm^-1
# Hindered rotor frequencies and barriers
7 cm^-1
50.0
50.0
50.0
50.0
50.0
300.0
300.0
7 cm^-1
932.1920503234123
932.1920503234123
932.1920503234123
932.1920503234123
932.1920503234123
10000.0
10000.0
# Symmetry number
6

# Species identifier (128 characters or less, no spaces)
C6H8(264)
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 165820.32182800144
# Thermodynamics data:
#   Standard enthalpy of formation; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#   Standard entropy of formation; allowed units are permutations of energy (J, kJ, cal, or kcal) and temperature (K, C, F, or R)
#   Heat capacity at 300, 400, 500, 600, 800, 1000, and 1500 K
J/mol 165820.32182800144
J/mol*K 331.96400557596087
7 J/mol*K
117.31936
150.12192000000002
175.81168
195.30912
224.01136000000002
244.764
277.39920000000006
# Species gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 80.0
m 5.865010633325628E-10
J 4.989907384649363E-21
# Harmonic oscillators; allowed units are Hz and cm^-1
34 cm^-1
2950.0
3000.0
3050.0
3100.0
1330.0
1430.0
900.0
1050.0
1000.0
1050.0
2995.0
3005.0
3015.0
3025.0
975.0
983.3333333333334
991.6666666666667
1000.0000000000001
1300.0
1325.0
1350.0
1375.0
400.0
433.3333333333333
466.66666666666663
499.99999999999994
1630.0
1646.6666666666667
1663.3333333333335
1680.0000000000002
180.78761624296342
180.78761624296342
180.78761624296342
180.78761624296342
# Rigid rotors; allowed units are Hz and cm^-1
0 cm^-1
# Hindered rotor frequencies and barriers
2 cm^-1
180.0
150.0
2 cm^-1
1709.1637970718484
10000.0
# Symmetry number
2

# Species identifier (128 characters or less, no spaces)
C6H9J(15)
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 159963.26130550657
# Thermodynamics data:
#   Standard enthalpy of formation; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
#   Standard entropy of formation; allowed units are permutations of energy (J, kJ, cal, or kcal) and temperature (K, C, F, or R)
#   Heat capacity at 300, 400, 500, 600, 800, 1000, and 1500 K
J/mol 159963.26130550657
J/mol*K 353.078601800321
7 J/mol*K
116.27336000000003
148.36464
175.47696000000002
198.44712
233.21616000000006
259.07328
300.66223999999994
# Species gas parameters
#   Molecular weight; allowed units are g/mol or u
#   Lennard-Jones sigma parameter; allowed units are m or A
#   Lennard-Jones epsilon parameter; allowed units are J or K
u 81.0
m 5.932967927172225E-10
J 5.0368332472871756E-21
# Harmonic oscillators; allowed units are Hz and cm^-1
36 cm^-1
2750.0
2800.0
2850.0
1350.0
1500.0
750.0
1050.0
1375.0
2995.0
3005.0
3015.0
3025.0
975.0
983.3333333333334
991.6666666666667
1000.0000000000001
1300.0
1325.0
1350.0
1375.0
400.0
433.3333333333333
466.66666666666663
499.99999999999994
1630.0
1646.6666666666667
1663.3333333333335
1680.0000000000002
3000.0
3100.0
440.0
815.0
1455.0
663.3481775698752
662.8607117857006
664.3028673161527
# Rigid rotors; allowed units are Hz and cm^-1
0 cm^-1
# Hindered rotor frequencies and barriers
3 cm^-1
50.0
300.0
300.0
3 cm^-1
1294.687714644968
7267.850355601379
7267.850355601379
# Symmetry number
6

# The number of isomers in the network (minimum of 2)
1
# The number of reactant channels in the network
1
# The number of product channels in the network
0

# The number and identifiers of each species in the isomer
1 C12H17J(375)

# The number and identifiers of each species in the isomer
2 C6H8(264) C6H9J(15)

# The number of reactions in the network (minimum of 2)
1

# The reaction equation, in the form A + B --> C + D
C12H17J(375) (included =false) <=> C6H8(264) + C6H9J(15) (included =true)
# Indices of the reactant and product isomers, starting with 1
1 2
# Ground-state energy; allowed units are J/mol, kJ/mol, cal/mol, kcal/mol, or cm^-1
J/mol 409463.12670332333
# High-pressure-limit kinetics model k(T):
#   Option 1: Arrhenius
#   Arrhenius preexponential factor; allowed units are combinations of volume {m^3, L, or cm^3} and time {s^-1}
#   Arrhenius activation energy; allowed units are J/mol, kJ/mol, cal/mol, or kcal/mol
#   Arrhenius temperature exponent
Arrhenius
s^-1 5.4543166671264806E14
J/mol 140032.80771784857
0.0
jwallen commented 14 years ago

If you pull the latest changes you should see that we are finally catching the NullPointerException. It has been replaced with a PDepException and a better error message. We also realized that we haven't been checking stderr from fame, and when we do this we get the error:

Exception: Access Violation At line 310 of file network.f90 Traceback: not available, compile with -ftrace=frame or -ftrace=full

Now, line 310 of network.f90 is

allocate( hind(1:size(spec%spectral%hindFreq), 1:2) )

Staring at it in context, the source of the error is not immediately obvious to me. I will think about it some more.

jwallen commented 14 years ago

Okay, we may have finally gotten this issue fixed. I refactored the offending function to avoid the line of code that causes the access violation, and the new version seems to work for Greg. Pull the latest changes and give it a try. If it works then I will mark this bug as (finally) closed.

athlonshi commented 14 years ago

Josh, great job! The test case completed successfully on my Windows 7 system.

jwallen commented 14 years ago

Excellent. We also have a better error system in place in case there are any other related problems in the future.

Closed by b7ab8022fe9f1cf2a4177c6cca392f97ee02c252.