GreenGroup/RMG-Java — Issue #233: NegativeRateException thrown
Author: nickvandewiele
Created: 2011-12-06 10:29:46+00:00
State: open

Hi,

while using RMG-Java at commit 898da5e9 I encountered the following error:

```
Solving reaction system...
ERROR: jing.rxn.NegativeRateException: JP10R6(14)+SPC(2778)=SPC(4728)+SPC(1074) 1.233e+10 0.89 19.23 !H_Abstraction estimate: (Average of: (Average of: (Average of: (Cd_pri O2b) && Average of: (Cd/H/NonDeC O2b) && Cd_pri H_rad && Average of: (Cd/H/NonDeC H_rad && Cd/H/NonDeO H_rad && Cd/H/OneDe H_rad) && Average of: (Cd_pri C_methyl && Average of: (Cd_pri C_rad/H2/Cs && Cd_pri C_rad/H2/Cd && Cd_pri C_rad/H2/Ct) && Average of: (Cd_pri C_rad/H/NonDeC && Average of: (Cd_pri C_rad/H/OneDeC)) && Average of: (Average of: (Cd_pri C_rad/Cs3) && Average of: (Cd_pri C_rad/Cs2))) && Average of: (Cd/H/NonDeC C_methyl && Cd/H/OneDe C_methyl) && Average of: (Cd_pri Cd_pri_rad && Average of: (Cd_pri Cd_rad/NonDeC && Cd_pri Cd_rad/OneDe)) && Average of: (Cd/H/NonDeC Cd_pri_rad) && Average of: (Cd/H/NonDeC Ct_rad) && Average of: (Cd_pri O_pri_rad) && Average of: (Cd/H/NonDeC O_pri_rad)))) [ Y_rad , Cd/H/NonDeC ]: 0.0
at jing.rxnSys.JDAS.getEdgeReactionString(JDAS.java:830)
at jing.rxnSys.JDAS.getAutoEdgeReactionInfo(JDAS.java:852)
at jing.rxnSys.JDASSL.solve(JDASSL.java:200)
at jing.rxnSys.ReactionSystem.solveReactionSystem(ReactionSystem.java:1431)
at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1559)
at RMG.main(RMG.java:96)

CRITICAL: JP10R6(14)+SPC(2778)=SPC(4728)+SPC(1074) 1.233e+10 0.89 19.23 !H_Abstraction estimate: (Average of: (Average of: (Average of: (Cd_pri O2b) && Average of: (Cd/H/NonDeC O2b) && Cd_pri H_rad && Average of: (Cd/H/NonDeC H_rad && Cd/H/NonDeO H_rad && Cd/H/OneDe H_rad) && Average of: (Cd_pri C_methyl && Average of: (Cd_pri C_rad/H2/Cs && Cd_pri C_rad/H2/Cd && Cd_pri C_rad/H2/Ct) && Average of: (Cd_pri C_rad/H/NonDeC && Average of: (Cd_pri C_rad/H/OneDeC)) && Average of: (Average of: (Cd_pri C_rad/Cs3) && Average of: (Cd_pri C_rad/Cs2))) && Average of: (Cd/H/NonDeC C_methyl && Cd/H/OneDe C_methyl) && Average of: (Cd_pri Cd_pri_rad && Average of: (Cd_pri Cd_rad/NonDeC && Cd_pri Cd_rad/OneDe)) && Average of: (Cd/H/NonDeC Cd_pri_rad) && Average of: (Cd/H/NonDeC Ct_rad) && Average of: (Cd_pri O_pri_rad) && Average of: (Cd/H/NonDeC O_pri_rad)))) [ Y_rad , Cd/H/NonDeC ]: 0.0

RMG execution terminated at 2011-12-05 15:43:17
```

I haven't yet analyzed more rigorously what happened, but it seems to me that :
* "reasonable kinetic parameters" were assigned by the averaging scheme, eg non-negative activation barriers
* at the end of the comprehensive diagnostics it states : ```0.0``` I am unsure what the 0 refers to. this may be a clue of what's going on.

when browsing through the issues list, i haven't found an issue referring to the exception that was thrown here. Most of them apply to negative concentrations, or negative activation energies...

this run was without P-dep activated.

any recent modifications to the JDASSL (/wrapper) that could 've caused this?