ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database
Species index in libraries
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 127
- Forks
- 160
- Avg merge
- 6d 2h
- Merged PRs (30d)
- 2
Description
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?
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue names no source file, test, or entry point. Start by tracing Chemkin conversion and library species-label/index handling, then reproduce the NH2(46)/NCNO(46) collision from the supplied example. Done means distinct species remain distinguishable when the generated library is used by an RMG job.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100