Tried to determine nonincluded isomer with maximum leak flux, but no suitable nonincluded reaction has been found.

[mrharper]

MRH ran the following condition file:

// Database
Database: RMG_database

// Thermo libraries
PrimaryThermoLibrary:
Name: RMG old
Location: primaryThermoLibrary
END

PrimaryTransportLibrary:
END

ReadRestart: no
WriteRestart: no

// Initial conditions
TemperatureModel: Constant (K) 1000
PressureModel: Constant (atm) 1

// Maximum Number of ** per species - (leave out)

// InChI generation
InChIGeneration: off

// Reactants
InitialStatus:

(1) propane 0.1e-3 (mol/cm3)
1 C 0 {2,S}
2 C 0 {1,S} {3,S}
3 C 0 {2,S}

END

// Inerts
InertGas:
N2 1 (mol/cm3)
END

// Spectroscopic data estimator...
SpectroscopicDataEstimator: FrequencyGroups

// Pressure Dependence...
PressureDependence: ReservoirState
PDepKineticsModel: Chebyshev

FinishController:
(1) Goal Conversion: propane 0.5
// (1) Goal ReactionTime: 0.07 (sec)
(2) Error Tolerance: 0.15

// Simulator...
DynamicSimulator: DASSL
// TimeStep: 
Conversions: AUTO
Atol: 1e-18
Rtol: 1e-4

// Reactions...
PrimaryReactionLibrary:
END

// Seed Mechanisms...
SeedMechanism:
//Name: thiofene
//Location: thiofene
//GenerateReactions: no
END

// Units...
ChemkinUnits:
A: moles
Ea: kcal/mol

After adding 10 species and 34 reactions to the core, MRH receives an error message (the subject of this issue) in addition to the following:

PDepNetwork #6: Isomers: CH4(11) (included =true) HJ(5) + CH3J(2) (included =true) Path reactions: CH4(11) (included =true) --> HJ(5) + CH3J(2) (included =true) Net reactions: Nonincluded reactions: CH4(11) (included =true) --> HJ(5) + CH3J(2) (included =true)

MRH will address this issue shortly (in collaboration w/JWA).

[mrharper]

BUG FIX: Update Reaction Lists when species is added to core

When running a pdep job, the core can either be increased by adding a species from the edge to the core OR by exploring a network (which has the largest leak flux).

For one example (as mentioned in the Issue tracker), RMG decided that the methane (CH4) pdep network had the greatest leak flux; however, both sets of isomers, CH4 and CH3+H, were already included, meaning there should be no NonIncludedRxn in that particular network (and hence, no leak flux).

JWA and MRH determined that when a species was added from the edge to the core, RMG was not "refreshing" the pdep networks. RMG now refreshes the networks, via a call to the network.updateReactionLists method, after adding a species from the edge to the core AND after exploring the network with the greatest leak flux.

Closed by f80aed4600660d76faa70813d8e20ab313204ed1