GreenGroup/RMG-Java — Issue #242: NullPointerException at jing.rxn.PDepRateConstant.calculateRate (no TMIN/TMAX on PLOGs from seed?)
Author: rwest
Created: 2012-01-10 00:42:07+00:00
State: open

A file that has

* Pdep off
* Glarborg/C1 seed (which has some PLOG rates)

fails with the following on the first attempt to solve reaction systems:

``` java
Solving reaction system...
ERROR: Error with Reaction: CO(6)+OH(17)=CO2(2)+Hj(11)	0.000e+00	0.00	0.00	!Seed Mechanism: Glarborg_C1
PLOG / 0.001 9.30e+10 0.0 0.0 /
PLOG / 1.0 8.00e+10 0.0 0.0 /
PLOG / 3.0 7.00e+10 0.0 0.0 /
PLOG / 10.0 3.70e+12 0.0 12.518 /
PLOG / 20.0 2.90e+12 0.0 11.922 /
PLOG / 50.0 1.50e+12 0.0 13.909 /
PLOG / 80.0 1.50e+11 0.0 1.987 /
PLOG / 100.0 1.50e+11 0.0 1.987 /
PLOG / 650.0 2.30e+11 0.2 4.968 /
PLOG / 2000.0 3.70e+07 1.34 2.186 /
DUP
CO(6)+OH(17)=CO2(2)+Hj(11)	0.000e+00	0.00	0.00	!Seed Mechanism: Glarborg_C1
PLOG / 0.001 7.10e+05 1.8 1.133 /
PLOG / 1.0 8.80e+05 1.77 0.9540000000000001 /
PLOG / 3.0 2.90e+05 1.9 0.397 /
PLOG / 10.0 9.30e+07 1.1 0.0 /
PLOG / 20.0 4.50e+07 1.2 0.0 /
PLOG / 50.0 5.80e+06 1.5 0.0 /
PLOG / 80.0 2.50e+05 1.9 0.0 /
PLOG / 100.0 1.90e+05 1.94 0.0 /
PLOG / 650.0 7.00e+05 1.7 0.298 /
PLOG / 2000.0 0.00e+00 0.0 0.0 /
DUP
! For the above reaction, deltaHrxn(T=298K) = -25.2 kcal/mol

ERROR: java.lang.NullPointerException
at jing.rxn.PDepRateConstant.calculateRate(PDepRateConstant.java:201)
at jing.rxn.PDepReaction.calculateRate(PDepReaction.java:360)
at jing.rxnSys.JDAS.transferReaction(JDAS.java:652)
at jing.rxnSys.JDAS.generatePDepODEReactionList(JDAS.java:167)
at jing.rxnSys.JDASSL.solve(JDASSL.java:161)
at jing.rxnSys.ReactionSystem.solveReactionSystem(ReactionSystem.java:1431)
at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1424)
at RMG.main(RMG.java:96)
```

A brief look at https://github.com/GreenGroup/RMG-Java/blob/master/source/RMG/jing/rxn/PDepRateConstant.java#L201
makes me guess that we aren't setting TMIN and TMAX for the PLOG rates from a seed mechanism?