ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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RMG should use high-P limit isomerization\association\dissociation library reactions in PDep exploration #1313

Closed alongd closed 6 years ago

alongd commented 6 years ago

I'm transferring an issue originally opened on the database repository to the Py repository:

We should allow RMG to use high-P limit isomerization\association\dissociation library reactions, if available.

To illustrate this problem for one case: RMG finds the network HSS + H <=> HSSH, but it won't further expand it to HSS + H <=> HSSH <=> H2SS <=> H2S + S

While the relevant high-P isomerization kinetics is available from a library:

entry(
    index = 66,
    label = "HSSH <=> H2SS",
    degeneracy = 2,
    kinetics = Arrhenius(A=(6.74e+12, 's^-1'), n=0.213, Ea=(193, 'kJ/mol'), T0=(1, 'K')),
    shortDesc = u"""[Sendt2009b]""",
    longDesc =
u"""
Table 1, R4
calculations done at the MRCI/aug-cc-pV(Q+d)Z//CASSCF/cc-pVTZ level of theory
""",
)
alongd commented 6 years ago

We should also use high-P limit rates from Troe/Lindemann expressions from libraries in our PDep network when available (originally issue #1294, relocated here)

alongd commented 6 years ago

For future debugging, I'm documenting here cases in which RMG did not take a high-P limit rate from a library for a PDep job:

primarySulfurLibrary

entry(
    index = 66,
    label = "HSSH <=> H2SS",
    degeneracy = 2,
    kinetics = Arrhenius(A=(6.74e+12, 's^-1'), n=0.213, Ea=(193, 'kJ/mol'), T0=(1, 'K')),
    shortDesc = u"""[Sendt2009b]""",
    longDesc =
u"""
Table 1, R4
calculations done at the MRCI/aug-cc-pV(Q+d)Z//CASSCF/cc-pVTZ level of theory
""",
)

This rate was never added to any relevant networks. Perhaps either because RMG doesn't have the template for it, or another more general problem of incorporating library reactions in networks.

alongd commented 6 years ago

Closed via #1357