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Species index in libraries

Open HiroumiTani opened this issue 7 years ago • 0 comments
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I converted a Chemkin file generaged by RMG to a new library. Because species in a Chemikin file had indexes, their indexes were reflected to labels of reactions in a new library of kinetics and thermo as shown below.

entry(
    index = 1,
    label = "NH2(46) + NH2(46) <=> N2H3(58) + H(8)",
    degeneracy = 1.0,
    kinetics = Chebyshev(
        coeffs = [
            [6.844, -7.326e-06, -1.245e-06, -1.424e-07],
            [3.05, 7.244e-06, 1.231e-06, 1.408e-07],
            [0.123, 5.578e-07, 9.478e-08, 1.084e-08],
            [0.04916, -4.475e-07, -7.603e-08, -8.695e-09],
            [0.01741, -2.781e-07, -4.724e-08, -5.403e-09],
            [0.006903, -6.777e-09, -1.153e-09, -1.321e-10],
        ],
        kunits = 'cm^3/(mol*s)',
        Tmin = (500, 'K'),
        Tmax = (3000, 'K'),
        Pmin = (0.493, 'atm'),
        Pmax = (1.974, 'atm'),
    ),
)

NH2 has an index of (46) in the library. Actually, it is just a part of the name of species. But, when I used the this library for a RMG job, RMG handles another species with the same index as well. In my case, NCNO has the same index of (46). A part of RMG.log are shown here.

3 network information
---------------------
Isomers:
    hydrazine(1)                                          86.2423 kJ/mol
Reactant channels:
    NCNO(46) + NCNO(46)                                   616.252 kJ/mol
    NH2(46) + NH2(46)                                     352.223 kJ/mol
Product channels:
    N2H3(58) + H(8)                                       425.149 kJ/mol
Path reactions:
    NCNO(46) + NCNO(46) <=> hydrazine(1)                   617.94 kJ/mol
    hydrazine(1) <=> NH2(46) + NH2(46)                     364.75 kJ/mol
    hydrazine(1) <=> N2H3(58) + H(8)                      425.149 kJ/mol

RMG mixes up two species with the same index. Probably, NH2(46) derived from the library should have a different index like NH2(46)(99). Otherwise, users should remove the indexes from the Chemkin files before converting to libraries. Could you solve this problem?

HiroumiTani avatar Feb 28 '18 22:02 HiroumiTani