ReactionMechanismGenerator / RMG-Java

The Java version of RMG: Reaction Mechanism Generator
http://rmg.sourceforge.net/
MIT License
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Error running the ODESolver: * MATRIX IS SINGULAR #51

Closed jdmo closed 14 years ago

jdmo commented 14 years ago

The end of the log file states this:

Reaction System 1 has not reached its termination criterion
although it seems to be valid (complete), so it was not interrupted for being invalid.
This probably means there was an error with the ODE solver, and we risk entering an endless loop.
Stopping.
Exception in thread "main" java.lang.Error
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1648)
    at RMG.main(RMG.java:57)

But the important error message to look for is a little bit earlier in the log file, where the ODE slover failed:

Error running the ODESolver: ***MESSAGE FROM ROUTINE DDASSL IN LIBRARY SLATEC.
Error running the ODESolver: ***POTENTIALLY RECOVERABLE ERROR, PROGRAM CONTINUES.
Error running the ODESolver: *  AT T =    6.782296D-05  AND STEPSIZE H =    8.463099D-09  THE ITERATION
Error running the ODESolver: *  MATRIX IS SINGULAR
Error running the ODESolver: *  ERROR NUMBER = -8
Error running the ODESolver: *
Error running the ODESolver: ***END OF MESSAGE
Error running the ODESolver: 
Error running the ODESolver: ******ODESOLVER FAILED : IDID= -8
ODE solver integrated to 6.782295851186213E-5 sec.

This was a job which used to run OK.

jdmo commented 14 years ago

this was the condition file:


Database: RMG_database

//MaxCarbonNumberPerSpecies: 
//MaxOxygenNumberPerSpecies: 
//MaxRadicalNumberPerSpecies: 
//MaxSulfurNumberPerSpecies: 
//MaxSiliconNumberPerSpecies: 
//MaxHeavyAtomPerSpecies:

PrimaryThermoLibrary:
Name: GRIMech3.0
Location: GRI-Mech3.0
Name: RMG-old
Location: primaryThermoLibrary
END

PrimaryTransportLibrary:
Name: GRIMech3.0
Location: GRI-Mech3.0
END

ReadRestart: no
WriteRestart: yes

TemperatureModel: Constant (K) 650 900 1350 1400
PressureModel: Constant (atm) 1 

InitialStatus:

(1) BUTEN 4.2509e-2 (mol/cm3)
1 C 0 {2,S}
2 C 0 {1,S} {3,D}
3 C 0 {2,D} {4,S}
4 C 0 {3,S} {5,S}
5 O 0 {4,S}

(2) O2 0.2338 (mol/cm3)
1 O 0 {2,D}
2 O 0 {1,D}

END

InertGas:
N2 0.8797 (mol/cm3)
Ar 0.0e-6 (mol/cm3)
END

SpectroscopicDataEstimator: FrequencyGroups
PressureDependence: ModifiedStrongCollision
PDepKineticsModel: Chebyshev
TRange: (K) 300 2100 8 4
PRange: (atm) 0.01 100 5 4

FinishController:
(1) Goal Conversion: BUTEN 0.99
(2) Error Tolerance: 0.05

DynamicSimulator: DASSL
Conversions: AUTO
Atol: 1e-24
Rtol: 1e-12

PrimaryReactionLibrary:
//Name: RMG-example
//Location: RMG_database/primaryReactionLibrary/Example
END

SeedMechanism:
Name: GRIMech3.0
Location: GRI-Mech3.0
GenerateReactions: no
//Name: Leeds
//Location: RMG_database/SeedMechanisms/combustion_core/version5
END

ChemkinUnits:
A: moles
Ea: kcal/mol

When it died, The model core has 268 reactions and 39 species.

gmagoon commented 14 years ago

Do you remember (or have a file from) when it last worked? Thanks, Greg

jdmo commented 14 years ago

I do! Which files would you like?

jdmo commented 14 years ago

The outANDerror.txt files, the script file, and the ODESolver folders are all at:

http://web.mit.edu/jdmo/Public/

gmagoon commented 14 years ago

It looks like the mechanisms differ between the case that fails and the case that does (at an equivalent model size to the point of failure of the other case; see output below), so it is not unexpected that it fails with a different mechanism. As to why it is a different mechanism, either there was one or more database/algorithmic changes or it is some non-deterministic thing. For the case that works:

ODE solver integrated to 1.160507608746159E-5 sec.
After ODE: from 0.0 SEC to 1.160507608746159E-5SEC
Sp.#    Name            Concentration   Flux
   1    BUTEN            3.183558E-07   -2.498431E-04
   2    O2               1.759307E-06   -1.881664E-04
  15    C3H8             4.394900E-36    2.953198E-30
  11    CH3CHO           3.179544E-18    6.383927E-13
   6    CH2CO            3.625784E-16    7.308602E-11
   3    C                1.699982E-30    5.722167E-25
  27    CO2              1.641967E-19    5.343214E-14
  34    O                3.183822E-12    1.960495E-07
  28    H                9.574475E-12    5.394126E-07
  14    HCCO             1.013515E-19    3.024438E-14
  21    CH3O             1.149533E-22    4.507423E-17
  31    H2O2             3.276897E-10    6.090131E-05
  30    H2O              3.021740E-10    5.667741E-05
   4    C2H              3.492074E-22    1.011586E-16
  32    OH               3.362239E-10    3.094830E-05
  17    CH2(S)           5.125426E-24    1.872102E-18
  25    HCO              2.008242E-18    2.165933E-13
   9    CH2CHO           2.291395E-17    2.364630E-12
  33    HO2              6.207609E-10    7.226317E-05
  19    CH2O             2.180904E-16    4.222532E-11
  10    C2H4             7.135762E-18    1.400187E-12
  23    CH4              3.777090E-20    1.378081E-14
   8    C2H3             1.808816E-17    1.819174E-12
  20    CH3              3.334793E-20    9.241970E-15
  24    CH3OH            1.038500E-21    3.066097E-16
   5    C2H2             5.722616E-17    1.125942E-11
  18    CH2              1.604753E-21    3.067431E-16
  16    CH               8.964699E-26    2.509318E-20
   7    HCCOH            4.402272E-21    1.658047E-15
  29    H2               5.744924E-10    7.583033E-05
  13    C2H6             2.239870E-24    8.851337E-19
  12    C2H5             3.173026E-23    9.706525E-18
  22    CH2OH            9.871568E-21    1.950634E-15
  26    CO               2.362230E-16    4.795214E-11
  38    C4H7OJ           7.614651E-12    6.471450E-07
  77    C4H7J            4.662439E-11   -4.972166E-07
 259    C4H6O            1.315725E-09    2.098821E-04
 540    C4H5OJ           3.387210E-12    1.098801E-06
 451    C4H6             3.397100E-10    3.367910E-05
For reaction system: 1 out of 4
At this time: 0.012366938069836355SEC
Conversion of BUTEN is:4.734022062469201E-5
For reaction system: 2 out of 4
At this time: 0.0010915434701134978SEC
Conversion of BUTEN is:0.001017393420199908
For reaction system: 3 out of 4
At this time: 8.539521090023828E-6SEC
Conversion of BUTEN is:0.0011697740262888168
For reaction system: 4 out of 4
At this time: 1.160507608746159E-5SEC
Conversion of BUTEN is:0.005477623978266455
Running Time is: 17.96405 minutes.
The model edge has 1991 reactions and 978 species.
For reaction system: 1 out of 4

For the case that fails:

ODE solver integrated to 2.649981635116006E-10 sec.
After ODE: from 0.0 SEC to 2.649981635116006E-10SEC
Sp.#    Name            Concentration   Flux
   1    BUTEN            3.201092E-07   -1.320660E-04
   2    O2               1.760605E-06   -4.103725E-05
  15    C3H8             7.050894E-50    2.143140E-39
  11    CH3CHO           1.036735E-52    2.753101E-42
   6    CH2CO            8.475318E-50    2.248070E-39
   3    C                1.030324E-28    1.166729E-18
  27    CO2              7.125179E-50    1.890471E-39
  34    O                1.763691E-25    1.996698E-15
  35    O2               3.740289E-25    4.204128E-15
  28    H                2.513998E-15    9.476812E-06
  14    HCCO             2.539939E-61    8.758249E-51
  21    CH3O             4.561408E-29    6.884217E-19
  31    H2O2             7.291639E-20    5.503120E-10
  30    H2O              3.825712E-19    2.887338E-09
   4    C2H             -1.094644E-87   -1.186838E-76
  32    OH               2.638247E-14    9.955571E-05
  17    CH2(S)           1.493056E-28    2.253397E-18
  25    HCO              3.560725E-28    4.030764E-18
   9    CH2CHO           9.843642E-47    2.233044E-36
  33    HO2              5.028416E-15    1.897501E-05
  19    CH2O             3.536251E-30    5.338166E-20
  10    C2H4             1.029661E-28    1.165657E-18
  23    CH4              1.319617E-22    1.493887E-12
   8    C2H3             3.561252E-28    4.031560E-18
  20    CH3              3.593141E-18    2.711716E-08
  24    CH3OH            8.760414E-30    1.322180E-19
   5    C2H2             7.805814E-57    8.463245E-46
  18    CH2              5.515809E-30    8.303647E-20
  16    CH               9.332771E-32    1.056527E-21
   7    HCCOH            3.545996E-66    1.222634E-55
  29    H2               2.661370E-18    2.007887E-08
  13    C2H6             1.959085E-33    3.698081E-23
  12    C2H5             2.137050E-34    4.033995E-24
  22    CH2OH            3.702377E-30    5.587762E-20
  26    CO               6.799552E-46    7.372233E-35
  39    C4H7OJ           7.544671E-15    2.846885E-05
  78    C4H7J            2.638285E-14    9.955860E-05
 150    C4H8O            2.792576E-20    2.107575E-10
 635    C3H4O            3.593273E-18    2.711866E-08
For reaction system: 1 out of 4
At this time: 6.782295851186213E-5SEC
Conversion of BUTEN is:2.8639113192063803E-8
For reaction system: 2 out of 4
At this time: 9.313984141764559E-7SEC
Conversion of BUTEN is:1.6746269282386095E-7
For reaction system: 3 out of 4
At this time: 3.5994823096230523E-10SEC
Conversion of BUTEN is:6.05766025119081E-8
For reaction system: 4 out of 4
At this time: 2.649981635116006E-10SEC
Conversion of BUTEN is:1.0931883787090868E-7
Running Time is: 13.291766666666666 minutes.
The model edge has 1714 reactions and 760 species.
For reaction system: 1 out of 4
The model core has 268 reactions and 39 species.
gmagoon commented 14 years ago

one additional line I forgot for the case that works:

The model core has 321 reactions and 39 species.
gmagoon commented 14 years ago

So far it looks like 9a94853c501d3572ac8b5c53fd92d01becb508e0 from May 21, 2010 is behaving similar to the case that works.

gmagoon commented 14 years ago

It looks like 1bcc6e44619fa54cf1f7762d93204468169a8cff from May 26, 2010 is working as well.

gmagoon commented 14 years ago

Revision 6492bf274287d941b175509bc7eb812ebd08a4b2 from May 30, 2010 fails but there are no ODE solver errors:

ODE solver integrated to 0.0 sec.
After ODE: from 0.0 SEC to 0.0SEC
Sp.#    Name            Concentration   Flux
   1    BUTEN            6.894661E-07   -1.634970E-11
   2    O2               3.792072E-06   -1.634970E-11
  15    C3H8             0.000000E+00    0.000000E+00
  11    CH3CHO           0.000000E+00    0.000000E+00
   6    CH2CO            0.000000E+00    0.000000E+00
   3    C                0.000000E+00    0.000000E+00
  27    CO2              0.000000E+00    0.000000E+00
  34    O                0.000000E+00    7.908684E-35
  28    H                0.000000E+00    1.129741E-19
  14    HCCO             0.000000E+00    0.000000E+00
  21    CH3O             0.000000E+00    0.000000E+00
  31    H2O2             0.000000E+00    0.000000E+00
  30    H2O              0.000000E+00    0.000000E+00
   4    C2H              0.000000E+00    0.000000E+00
  32    OH               0.000000E+00    3.193239E-18
  17    CH2(S)           0.000000E+00    0.000000E+00
  25    HCO              0.000000E+00    0.000000E+00
   9    CH2CHO           0.000000E+00    0.000000E+00
  33    HO2              0.000000E+00    1.634970E-11
  19    CH2O             0.000000E+00    0.000000E+00
  10    C2H4             0.000000E+00    0.000000E+00
  23    CH4              0.000000E+00    0.000000E+00
   8    C2H3             0.000000E+00    0.000000E+00
  20    CH3              0.000000E+00    0.000000E+00
  24    CH3OH            0.000000E+00    0.000000E+00
   5    C2H2             0.000000E+00    0.000000E+00
  18    CH2              0.000000E+00    0.000000E+00
  16    CH               0.000000E+00    0.000000E+00
   7    HCCOH            0.000000E+00    0.000000E+00
  29    H2               0.000000E+00    0.000000E+00
  13    C2H6             0.000000E+00    0.000000E+00
  12    C2H5             0.000000E+00    0.000000E+00
  22    CH2OH            0.000000E+00    0.000000E+00
  26    CO               0.000000E+00    0.000000E+00
  38    C4H7OJ           0.000000E+00    1.634970E-11
  77    C4H7J            0.000000E+00    3.193239E-18
 260    C4H6O            0.000000E+00    0.000000E+00
ODE solver integrated to 0.0 sec.
After ODE: from 0.0 SEC to 0.0SEC
Sp.#    Name            Concentration   Flux
   1    BUTEN            4.979477E-07   -9.115723E-09
   2    O2               2.738718E-06   -9.082121E-09
  15    C3H8             0.000000E+00    0.000000E+00
  11    CH3CHO           0.000000E+00    0.000000E+00
   6    CH2CO            0.000000E+00    0.000000E+00
   3    C                0.000000E+00    0.000000E+00
  27    CO2              0.000000E+00    0.000000E+00
  34    O                0.000000E+00    3.626333E-24
  28    H                0.000000E+00    1.918116E-12
  14    HCCO             0.000000E+00    0.000000E+00
  21    CH3O             0.000000E+00    0.000000E+00
  31    H2O2             0.000000E+00    0.000000E+00
  30    H2O              0.000000E+00    0.000000E+00
   4    C2H              0.000000E+00    0.000000E+00
  32    OH               0.000000E+00    3.834690E-11
  17    CH2(S)           0.000000E+00    0.000000E+00
  25    HCO              0.000000E+00    0.000000E+00
   9    CH2CHO           0.000000E+00    0.000000E+00
  33    HO2              0.000000E+00    9.073978E-09
  19    CH2O             0.000000E+00    0.000000E+00
  10    C2H4             0.000000E+00    0.000000E+00
  23    CH4              0.000000E+00    0.000000E+00
   8    C2H3             0.000000E+00    0.000000E+00
  20    CH3              0.000000E+00    0.000000E+00
  24    CH3OH            0.000000E+00    0.000000E+00
   5    C2H2             0.000000E+00    0.000000E+00
  18    CH2              0.000000E+00    0.000000E+00
  16    CH               0.000000E+00    0.000000E+00
   7    HCCOH            0.000000E+00    0.000000E+00
  29    H2               0.000000E+00    0.000000E+00
  13    C2H6             0.000000E+00    0.000000E+00
  12    C2H5             0.000000E+00    0.000000E+00
  22    CH2OH            0.000000E+00    0.000000E+00
  26    CO               0.000000E+00    0.000000E+00
  38    C4H7OJ           0.000000E+00    9.075896E-09
  77    C4H7J            0.000000E+00    3.834690E-11
 260    C4H6O            0.000000E+00    0.000000E+00
ODE solver integrated to 0.0 sec.
After ODE: from 0.0 SEC to 0.0SEC
Sp.#    Name            Concentration   Flux
   1    BUTEN            3.319652E-07   -4.367874E-05
   2    O2               1.825812E-06   -1.001686E-05
  15    C3H8             0.000000E+00    0.000000E+00
  11    CH3CHO           0.000000E+00    0.000000E+00
   6    CH2CO            0.000000E+00    0.000000E+00
   3    C                0.000000E+00    0.000000E+00
  27    CO2              0.000000E+00    0.000000E+00
  34    O                0.000000E+00    4.271551E-15
  28    H                0.000000E+00    3.385761E-06
  14    HCCO             0.000000E+00    0.000000E+00
  21    CH3O             0.000000E+00    0.000000E+00
  31    H2O2             0.000000E+00    0.000000E+00
  30    H2O              0.000000E+00    0.000000E+00
   4    C2H              0.000000E+00    0.000000E+00
  32    OH               0.000000E+00    3.695083E-05
  17    CH2(S)           0.000000E+00    0.000000E+00
  25    HCO              0.000000E+00    0.000000E+00
   9    CH2CHO           0.000000E+00    0.000000E+00
  33    HO2              0.000000E+00    1.858886E-06
  19    CH2O             0.000000E+00    0.000000E+00
  10    C2H4             0.000000E+00    0.000000E+00
  23    CH4              0.000000E+00    0.000000E+00
   8    C2H3             0.000000E+00    0.000000E+00
  20    CH3              0.000000E+00    0.000000E+00
  24    CH3OH            0.000000E+00    0.000000E+00
   5    C2H2             0.000000E+00    0.000000E+00
  18    CH2              0.000000E+00    0.000000E+00
  16    CH               0.000000E+00    0.000000E+00
   7    HCCOH            0.000000E+00    0.000000E+00
  29    H2               0.000000E+00    0.000000E+00
  13    C2H6             0.000000E+00    0.000000E+00
  12    C2H5             0.000000E+00    0.000000E+00
  22    CH2OH            0.000000E+00    0.000000E+00
  26    CO               0.000000E+00    0.000000E+00
  38    C4H7OJ           0.000000E+00    5.244647E-06
  77    C4H7J            0.000000E+00    3.695083E-05
 260    C4H6O            0.000000E+00    0.000000E+00
ODE solver integrated to 0.0 sec.
After ODE: from 0.0 SEC to 0.0SEC
Sp.#    Name            Concentration   Flux
   1    BUTEN            3.201093E-07   -1.140157E-04
   2    O2               1.760605E-06   -2.440607E-05
  15    C3H8             0.000000E+00    0.000000E+00
  11    CH3CHO           0.000000E+00    0.000000E+00
   6    CH2CO            0.000000E+00    0.000000E+00
   3    C                0.000000E+00    0.000000E+00
  27    CO2              0.000000E+00    0.000000E+00
  34    O                0.000000E+00    1.853399E-14
  28    H                0.000000E+00    9.514452E-06
  14    HCCO             0.000000E+00    0.000000E+00
  21    CH3O             0.000000E+00    0.000000E+00
  31    H2O2             0.000000E+00    0.000000E+00
  30    H2O              0.000000E+00    0.000000E+00
   4    C2H              0.000000E+00    0.000000E+00
  32    OH               0.000000E+00    9.786363E-05
  17    CH2(S)           0.000000E+00    0.000000E+00
  25    HCO              0.000000E+00    0.000000E+00
   9    CH2CHO           0.000000E+00    0.000000E+00
  33    HO2              0.000000E+00    2.689114E-06
  19    CH2O             0.000000E+00    0.000000E+00
  10    C2H4             0.000000E+00    0.000000E+00
  23    CH4              0.000000E+00    0.000000E+00
   8    C2H3             0.000000E+00    0.000000E+00
  20    CH3              0.000000E+00    0.000000E+00
  24    CH3OH            0.000000E+00    0.000000E+00
   5    C2H2             0.000000E+00    0.000000E+00
  18    CH2              0.000000E+00    0.000000E+00
  16    CH               0.000000E+00    0.000000E+00
   7    HCCOH            0.000000E+00    0.000000E+00
  29    H2               0.000000E+00    0.000000E+00
  13    C2H6             0.000000E+00    0.000000E+00
  12    C2H5             0.000000E+00    0.000000E+00
  22    CH2OH            0.000000E+00    0.000000E+00
  26    CO               0.000000E+00    0.000000E+00
  38    C4H7OJ           0.000000E+00    1.220357E-05
  77    C4H7J            0.000000E+00    9.786363E-05
 260    C4H6O            0.000000E+00    0.000000E+00
For reaction system: 1 out of 4
At this time: 0.0SEC
Conversion of BUTEN is:0.0
For reaction system: 2 out of 4
At this time: 0.0SEC
Conversion of BUTEN is:0.0
For reaction system: 3 out of 4
At this time: 0.0SEC
Conversion of BUTEN is:-2.220446049250313E-16
For reaction system: 4 out of 4
At this time: 0.0SEC
Conversion of BUTEN is:0.0
Running Time is: 10.210783333333334 minutes.
The model edge has 1439 reactions and 667 species.
For reaction system: 1 out of 4
The model core has 263 reactions and 37 species.
For reaction system: 2 out of 4
The model core has 263 reactions and 37 species.
For reaction system: 3 out of 4
The model core has 263 reactions and 37 species.
For reaction system: 4 out of 4
The model core has 263 reactions and 37 species.
After garbage collection:
Memory used: 331415552
Free memory: 294960632
Reaction System 1 has not reached its termination criterion
although it seems to be valid (complete), so it was not interrupted for being invalid.
This probably means there was an error with the ODE solver, and we risk entering an endless loop.
Stopping.
Exception in thread "main" java.lang.Error
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1648)
        at RMG.main(RMG.java:57)
gmagoon commented 14 years ago

Revision f2c35559c6c0389bb266cdd02803da8e60ff5fe1 on debugging branch seems to work. It is beginning to look like 2e1668d3d1ade39194ed69bb1d8b882b59fdff20 may be the problematic commit that is causing "infinite loop" error termination (suspected to be due to inconsistencies between Java flux calculation and Fortran flux calculation; evidence: "infinite loop" error without ODESolver error as noted above and ODESolver failed error without infinite loop termination, as occurs in some of the earlier iterations in Jeff's latest files in his Athena locker.) (It is still not clear what causes the ODESolver error in the first place.)

gmagoon commented 14 years ago

Revision 8cc7ecd0b2fc2e84101ad784e8fd1069503c33ec on debugging branch "issue51debug" seems to work, as well, suggesting 2e1668d isn't the problematic commit after all.

gmagoon commented 14 years ago

Revision e3165aa31b7bec365e127fc65c61b0ac04780621 fails due to null pointer exception (roughly in the region where infinite loop failure occurs in other revisions...I may need to look closer to confirm). Revision d80450f6d1c860407fe403e87060c48a78631dce will be applied next to address NPE.

gmagoon commented 14 years ago

In revision 9ba6bdffc8edb2cb0094bcc58e154a8030c34f36 , the job fails due to infinite loop error despite no ODESolver error. This suggests something in f0f3db70ffccfa4c76b03b158f4cf598cb40b2a6 , d00aee2cdfa92032b510731062a765c5ce4c608c , 4310cc20f6da8ea8a2800d6cb0191cb0b3f2e928 , and/or d80450f6d1c860407fe403e87060c48a78631dce is causing a discrepency between Java and Fortran flux estimates.

gmagoon commented 14 years ago

Revision a59fe9c3a09aaf4d54dd335722ecc44f8a5d9383 seems to be working, apparently ruling out the first two of the four commits previously mentioned (for giving rise to Java/Fortran flux discrepency).

gmagoon commented 14 years ago

Adding an extra debug output line to Fortran output and using a simplified condition file without Seed Mechanism (copied below) suggests that it is Edge Species 70 (C4H6) (and probably others) that "trip" the ODESolver to stop in 9ba6bdffc8edb2cb0094bcc58e154a8030c34f36 . Moreover, the reactant is #8 (C4H7O2) in the IDtranslator, which is unusual since there are only 7 species in the core...it looks like there may be an extra species that is incorrectly being added to the ID translator, (which I guess would be assigned an arbitrary, probably large, concentration value in the Fortran code if it is not initialized). More to follow, once I figure out why this is being included in IDTranslator...

//tracks the consumption of 1,3-hexadiene in presence of N2, Methane and hydrogen.
//notice the primary reaction library is turned off because this is not 
//a oxidation mechanism. Also the sensitivity analysis section is missing 
//because we are using the dassl solver.

Database: RMG_database

//MaxCarbonNumberPerSpecies: 
//MaxOxygenNumberPerSpecies: 
//MaxRadicalNumberPerSpecies: 
//MaxSulfurNumberPerSpecies: 
//MaxSiliconNumberPerSpecies: 
//MaxHeavyAtomPerSpecies:

PrimaryThermoLibrary:
Name: GRIMech3.0
Location: GRI-Mech3.0
Name: RMG-old
Location: primaryThermoLibrary
END

PrimaryTransportLibrary:
Name: GRIMech3.0
Location: GRI-Mech3.0
END

ReadRestart: no
WriteRestart: yes

TemperatureModel: Constant (K) 650 900 1350 1400
PressureModel: Constant (atm) 1 

InitialStatus:

(1) BUTEN 4.2509e-2 (mol/cm3)
1 C 0 {2,S}
2 C 0 {1,S} {3,D}
3 C 0 {2,D} {4,S}
4 C 0 {3,S} {5,S}
5 O 0 {4,S}

(2) O2 0.2338 (mol/cm3)
1 O 0 {2,D}
2 O 0 {1,D}

END

InertGas:
N2 0.8797 (mol/cm3)
Ar 0.0e-6 (mol/cm3)
END

SpectroscopicDataEstimator: FrequencyGroups
PressureDependence: ModifiedStrongCollision
PDepKineticsModel: Chebyshev
TRange: (K) 300 2100 8 4
PRange: (atm) 0.01 100 5 4

FinishController:
(1) Goal Conversion: BUTEN 0.99
(2) Error Tolerance: 0.05

DynamicSimulator: DASSL
Conversions: AUTO
Atol: 1e-24
Rtol: 1e-12

PrimaryReactionLibrary:
//Name: RMG-example
//Location: RMG_database/primaryReactionLibrary/Example
END

SeedMechanism:
//Name: GRIMech3.0
//Location: GRI-Mech3.0
//GenerateReactions: no
//Name: Leeds
//Location: RMG_database/SeedMechanisms/combustion_core/version5
END

ChemkinUnits:
A: moles
Ea: kcal/mol
gmagoon commented 14 years ago

It looks like C4H7O2J is being put in the IDTranslator becuase JDAS's getAutoEdgeReactionInfo() is implicitly assuming that all reactants in unreactedReactions are core species, and tries to get an EdgeID for it. In particular, JDAS's consideration of the following unreacted reaction : C4H7O2J(110) --> O2JJ(26) + C4H7J(11) results in C4H7O2J(110) being added to IDTranslator (though C4H7O2J(110) is not in the core; only C4H7J(11) is). A fix is in development to address this...

gmagoon commented 14 years ago

I think commit 687f30ad741eaf8650cb83a53180dfab405c9494 may address the issue of inconsistency between Java and Fortran edge flux evaluation. On the issue51debug branch (936992fb452c8b14b472d8de3a3e935fc0228787) the test job (sans Seed Mechanism) fails at a later point with the following error message. I'm thinking this issue may be addressed in one of the later fixes on the master branch

java.lang.NullPointerException
null
        at jing.rxn.FastMasterEqn.runPDepCalculation(FastMasterEqn.java:272)
        at jing.rxnSys.ReactionSystem.initializePDepNetwork(ReactionSystem.java:544)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1412)
        at RMG.main(RMG.java:57)
gmagoon commented 14 years ago

With commit 687f30ad741eaf8650cb83a53180dfab405c9494 , the issue with consistency between Java and Fortran seems to be eliminated. The test job (with seed mechanism) fails with an unrelated error that JWA is looking at:

jing.rxn.PDepException: Tried to determine nonincluded isomer with maximum leak flux, but no suitable nonincluded reaction has been found.
        at jing.rxn.PDepNetwork.getMaxLeakIsomer(PDepNetwork.java:531)
        at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:278)
        at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3992)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1408)
        at RMG.main(RMG.java:57)
Tried to determine nonincluded isomer with maximum leak flux, but no suitable nonincluded reaction has been found.
PDepNetwork #877:
        Isomers:
                C4H7OJ(35)
                C4H6(453) + OH(32)
        Path reactions:
                C4H7OJ(35) --> C4H6(453) + OH(32)
        Net reactions:
        Nonincluded reactions:
                C4H7OJ(35) --> C4H6(453) + OH(32)

There are also no ODESolver failures. However, jdmo reports that the ODESolver issues occur on the oxygen branch, so this may suggest a fundamental issue of stiffness, possibly related to new oxygen chemistry.

(Note: Contrary to my original understanding, implicit in some of my comments above, it seems that ODESolver failures without infinite loop termination may be "normal" (i.e. not indicative of Java/Fortran edge flux inconsistency), and the infinite loop termination only occurs when ALL of the reaction systems fail.)

gmagoon commented 14 years ago

Jeff, can we close this bug now? From what I recall, you sent an e-mail to rmg_dev suggesting you have worked around stiffness issues.

gmagoon commented 14 years ago

Closed per discussion with Jeff.