ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

BM Tree Fitting Gets Stuck in a Loop

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Python
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Description

I'm trying to refit the Disproportionation tree using some new training reactions I calculated. I tried using Matt's tree fitting script and it appears to be stuck in a loop. I don't know if I just haven't let it run long enough (tried 24 hours) or if there's a setting I need to change so it can break free.

I haven't figured out a good way to log the error, so here's a portion of what it keeps printing to the terminal:

3 *4 H u0 p0 c0 {1,S}
4    H u0 p0 c0 {1,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {2,S}
7    H u0 p0 c0 {2,S}

ERROR:root:C2H5-2
ERROR:root:C2H5-2
multiplicity 2
1    C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 *1 C u1 p0 c0 {1,S} {6,S} {7,S}
3    H u0 p0 c0 {1,S}
4    H u0 p0 c0 {1,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {2,S}
7    H u0 p0 c0 {2,S}

ERROR:root:C2H6
ERROR:root:C2H6
1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2    C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3    H u0 p0 c0 {1,S}
4    H u0 p0 c0 {1,S}
5 *4 H u0 p0 c0 {1,S}
6    H u0 p0 c0 {2,S}
7    H u0 p0 c0 {2,S}
8    H u0 p0 c0 {2,S}

ERROR:root:C2H4
ERROR:root:C2H4
1 *3 C u0 p0 c0 {2,D} {3,S} {4,S}
2 *2 C u0 p0 c0 {1,D} {5,S} {6,S}
3    H u0 p0 c0 {1,S}
4    H u0 p0 c0 {1,S}
5    H u0 p0 c0 {2,S}
6    H u0 p0 c0 {2,S}

ERROR:root:Clearing Regularization Dimensions and Reattempting

Any help here is appreciated, thanks!

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First steps

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  3. Fork the repository and make your change on a branch.
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Research direction

Start with scripts/BM tree fitting notebook.ipynb and reproduce the behavior using the training reactions from commit a78eea07fafeaf06d6558474e0a15a6ca74cf6e0. Inspect the repeated C2H5/C2H6/C2H4 errors and the regularization reset message; done means determining why fitting does not terminate and documenting or implementing a reliable resolution.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
data, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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