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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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IndexOutOfBoundsException in P-Dep operation when "Including" species #210

Open gmagoon opened 13 years ago

gmagoon commented 13 years ago

My P-Dep job (no restart or pruning) failed with the following...I don't think this has been reported before, but if there is already a reported issue on this, please let me know:

Created new species: C10H12JJ(12471)
Created new reverse BiradFromMultipleBond reaction: C10H12(7071) --> C10H12JJ(12471)
Created new reverse BiradFromMultipleBond reaction: C10H12(7071) --> C10H12JJ(7018)
Created new reverse BiradFromMultipleBond reaction: C10H12(7071) --> C10H12JJ(10943)
Created new reverse BiradFromMultipleBond reaction: C10H12(7071) --> C10H12JJ(11386)
Created new reverse BiradFromMultipleBond reaction: C10H12(7071) --> C10H12JJ(11982)

Add a new included species: C10H12(9781)
ERROR: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.LinkedList.entry(LinkedList.java:382)
    at java.util.LinkedList.get(LinkedList.java:332)
    at jing.rxnSys.RateBasedPDepRME.makeSpeciesIncluded(RateBasedPDepRME.java:373)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:239)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3894)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1464)
    at RMG.main(RMG.java:96)

CRITICAL: Index: 0, Size: 0

RMG execution terminated at 2011-09-02 23:02:53
gmagoon commented 13 years ago

This happened again:

Created new reverse BiradFromMultipleBond reaction: C8H12(4099) --> C8H12JJ(5186)

Add a new included species: C5H5CH3_2(86)

Network 4956 has been altered already this step, so will not be expanded until next step.

Add a new included species: C8H12(4875)
ERROR: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0         
    at java.util.LinkedList.entry(LinkedList.java:382)                
    at java.util.LinkedList.get(LinkedList.java:332)                  
    at jing.rxnSys.RateBasedPDepRME.makeSpeciesIncluded(RateBasedPDepRME.java:373)
    at jing.rxnSys.RateBasedPDepRME.enlargeReactionModel(RateBasedPDepRME.java:239)
    at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3917)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1487)
    at RMG.main(RMG.java:96)

CRITICAL: Index: 0, Size: 0

RMG execution terminated at 2011-09-28 19:52:12

Any tips, @jwallen?

gmagoon commented 13 years ago

Here is the final printout for all 18 reaction systems:

Enlarging reaction model   
Reaction system 1 of 18
Time: 4.5299e-06 s
Rmin: 2.1489e-04 mol/cm^3*s
Edge species C6H5OJ(4208) has highest flux: 1.9213e-04 mol/cm^3*s (0.894087)
Edge species C6H7O2J(4725) has highest leak flux: 2.1732e-04 mol/cm^3*s (1.011303)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 2 of 18
Time: 4.8905e-06 s
Rmin: 2.1982e-04 mol/cm^3*s
Edge species C6H5OJ(4208) has highest flux: 2.1695e-04 mol/cm^3*s (0.986946)
Edge species C6H7O2J(4725) has highest leak flux: 2.2365e-04 mol/cm^3*s (1.017409)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 3 of 18
Time: 5.4357e-06 s
Rmin: 1.8743e-04 mol/cm^3*s
Edge species C6H5OJ(4208) has highest flux: 1.9016e-04 mol/cm^3*s (1.014547)
Edge species C6H7O2J(4725) has highest leak flux: 1.7819e-04 mol/cm^3*s (0.950699)
Species C6H5OJ(4208) will be moved to the core.
Reaction system 4 of 18
Time: 2.4870e-06 s
Rmin: 1.1210e-03 mol/cm^3*s
Edge species C6H5OJ(4208) has highest flux: 5.5738e-04 mol/cm^3*s (0.497232)
Edge species C6H7O2J(4725) has highest leak flux: 1.1321e-03 mol/cm^3*s (1.009926)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 5 of 18
Time: 5.0808e-06 s
Rmin: 1.2556e-03 mol/cm^3*s
Edge species C6H5OJ(4208) has highest flux: 1.2652e-03 mol/cm^3*s (1.007614)
Edge species C6H7O2J(4725) has highest leak flux: 1.1461e-03 mol/cm^3*s (0.912824)
Species C6H5OJ(4208) will be moved to the core.
Reaction system 6 of 18
Time: 6.7794e-06 s
Rmin: 1.1321e-03 mol/cm^3*s
Edge species C6H5OJ(4208) has highest flux: 1.1374e-03 mol/cm^3*s (1.004727)
Edge species C6H5O2J(3874) has highest leak flux: 7.7223e-04 mol/cm^3*s (0.682136)
Species C6H5OJ(4208) will be moved to the core.
Reaction system 7 of 18
Time: 7.7720e-07 s
Rmin: 7.1868e-03 mol/cm^3*s
Edge species JP10R8(17) has highest flux: 4.3848e-03 mol/cm^3*s (0.610119)
Edge species C6H7O2J(4725) has highest leak flux: 7.2775e-03 mol/cm^3*s (1.012619)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 8 of 18
Time: 6.6273e-07 s
Rmin: 6.5105e-03 mol/cm^3*s
Edge species JP10R8(17) has highest flux: 3.5987e-03 mol/cm^3*s (0.552751)
Edge species C6H7O2J(4725) has highest leak flux: 6.6000e-03 mol/cm^3*s (1.013743)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 9 of 18
Time: 6.2789e-07 s
Rmin: 5.6404e-03 mol/cm^3*s
Edge species JP10R8(17) has highest flux: 2.7172e-03 mol/cm^3*s (0.481736)
Edge species C6H7O2J(4725) has highest leak flux: 5.6878e-03 mol/cm^3*s (1.008404)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 10 of 18
Time: 1.6480e-07 s
Rmin: 1.0580e-01 mol/cm^3*s
Edge species JP10R8(17) has highest flux: 5.8482e-02 mol/cm^3*s (0.552777)
Edge species C6H7O2J(4725) has highest leak flux: 1.0702e-01 mol/cm^3*s (1.011580)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 11 of 18
Time: 1.5345e-07 s
Rmin: 9.5897e-02 mol/cm^3*s
Edge species C10H16(1909) has highest flux: 4.9288e-02 mol/cm^3*s (0.513964)
Edge species C6H7O2J(4725) has highest leak flux: 9.5900e-02 mol/cm^3*s (1.000030)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 12 of 18
Time: 1.6023e-07 s
Rmin: 8.3436e-02 mol/cm^3*s
Edge species C10H16(1909) has highest flux: 4.0787e-02 mol/cm^3*s (0.488847)
Edge species C6H7O2J(4725) has highest leak flux: 8.4914e-02 mol/cm^3*s (1.017710)
The pressure-dependent network of C6H7O2J(4725) will be explored.
Reaction system 13 of 18
Time: 6.1891e-08 s
Rmin: 1.7942e-01 mol/cm^3*s
Edge species C8H12(4968) has highest flux: 1.0352e-01 mol/cm^3*s (0.576937)
Edge species C8H12(4099) has highest leak flux: 1.8221e-01 mol/cm^3*s (1.015545)
The pressure-dependent network of C8H12(4099) will be explored.
Reaction system 14 of 18
Time: 6.2892e-08 s
Rmin: 1.6362e-01 mol/cm^3*s
Edge species C8H12(4968) has highest flux: 9.4664e-02 mol/cm^3*s (0.578563)
Edge species C8H12(4099) has highest leak flux: 1.6663e-01 mol/cm^3*s (1.018406)
The pressure-dependent network of C8H12(4099) will be explored.
Reaction system 15 of 18
Time: 6.5287e-08 s
Rmin: 1.4165e-01 mol/cm^3*s
Edge species C8H12(4968) has highest flux: 8.1989e-02 mol/cm^3*s (0.578834)
Edge species C8H12(4099) has highest leak flux: 1.4432e-01 mol/cm^3*s (1.018883)
The pressure-dependent network of C8H12(4099) will be explored.
Reaction system 16 of 18
Time: 2.3893e-08 s
Rmin: 5.4404e+00 mol/cm^3*s
Edge species C8H12(4968) has highest flux: 3.9738e+00 mol/cm^3*s (0.730414)
Edge species C5H5CH3_2(86) has highest leak flux: 5.5454e+00 mol/cm^3*s (1.019304)
The pressure-dependent network of C5H5CH3_2(86) will be explored.
Reaction system 17 of 18
Time: 2.7188e-08 s
Rmin: 4.7293e+00 mol/cm^3*s
Edge species C8H12(4968) has highest flux: 4.2263e+00 mol/cm^3*s (0.893638)
Edge species C8H12(4875) has highest leak flux: 4.8854e+00 mol/cm^3*s (1.033006)
The pressure-dependent network of C8H12(4875) will be explored.
Reaction system 18 of 18
Time: 2.8720e-08 s
Rmin: 4.2491e+00 mol/cm^3*s
Edge species C8H12(4968) has highest flux: 3.7702e+00 mol/cm^3*s (0.887296)
Edge species C8H12(4875) has highest leak flux: 4.3582e+00 mol/cm^3*s (1.025674)
The pressure-dependent network of C8H12(4875) will be explored.
jwallen commented 13 years ago

I'm thinking this is simply an issue with multiple reaction systems, in that an earlier enlarge action in this step caused networks to be merged such that C8H12(4875) no longer exists as a nonincluded well. Therefore I am tentatively adding a commit that squashes this situation (with a warning message).

gmagoon commented 13 years ago

Great...thanks!