1. RMG Study Group/Meeting – Summary of the many Github issues and [hopefully] ways to resolve them March 14, 2014 Enoch Dames Note: Will someone please log notes from this meeting?

2. 232 unresolved issues on Github RMG-Py: 90 RMG-Java: 91 (some relevance to Py) RMG-Database: 14 Resolutions in progress with the Universal Database RMG-website: 37 Many similar issues and themes have been repeated over the last 4 years: 1.Symmetry and reaction path degeneracy 2.Aromaticity and Resonance 3.Pdep: failing solvers, invalid MCRCs 4.QM(TP) 5.Multiplicity 6.Documentation issues The good news: the most pressing issues are already being addressed! some of these issues may already be fixed, but remain open

3. 1. Symmetry, reaction path degeneracy, counting bond symmetry number unreliable #12Py overall symmetry number errors #24Py symmetry number of phenoxy radical is 1 (should be 2)#119Py ' RMG-Java still finds 2. so this means that the algorithm for calculating symmetry numbers is changed‘ Incorrect symmetry number for C6H10 species #80Java Reaction path degeneracy not properly treated #29Py: The kinetics in the database are given on a per-reaction site basis because the reaction path degeneracy varies with the species involved. To correct for this, we need to. multiply the rate from the database by the reaction path degeneracy But how do we determine this degeneracy? Unable to calculate degeneracy in reaction family Intra_R_Add_Endocyclic #69Py Chirality not taken into account #4Cantherm Rotor counting inaccurate for certain species with triple bonds #35Java Possible resolution(s) It was suggested: migrate symmetry perception algo's away from Molecule?#70Py These issues are currently being addressed separately in Py and Java

4. 2. Aromaticity & Resonance Aromaticity detection problems in thermo? #106Py - has this been fixed recently? Resonance isomers of oxygenated species #118Py Bi-radical / resonance of C4H4 (and similar things) #154Py Does RMG-Py allow adjlists with benzene bonds? #163Py Resonance in cyclic compounds #294Java "Other" group additivity thermo corrections not applied#285Java (note: the "other" groups currently contains corrections for cis double bonds, ketenes, and the ortho group) Resonance forms for benzyne and benzyne like molecules not identified #238Java Aromaticity perception doesn't work for naphthalene #223Java The issue of resonance isomer identification for dienes (along with recent bugfix in Java. Py?) #RMG Study Group 2/21/2014 Resolution(s) already being pursued

5. 3. Pdep and invalid/inaccurate MCRCs Pdep: #43Py and #44Py - negative rate coefficients for MSC and RS. Is anyone still seeing this? And if you are, is your thermo okay? Invalid k(E) values computed for path reaction. #77Py (re-read this one tomorrow) “This is especially true when using ILT to go from k(T) -> k(E), which by definition should yield the same k(T) at the end. Looking at the first example in the thread, I see that the barrier height is negative. Not sure if RMG-Py handles this correctly, especially because I'm not really sure how it should be handled.”  Machine precision an issue for rates that are smaller than e-40 for bimolecular? no units provided or this ex.  Jallen: The problem with this particular network is that the reaction H2CCCH C3H2+H, coming from Glarborg/C2, has an activation energy that is ~20 kcal/mol below the barrier height (as estimated from the enthalpy of reaction). Using the ILT method to get k(E) requires that the activation energy and the barrier height be the same. Since the k(T) estimate came from a library instead of an estimate, its Ea was not adjusted to be at least dHrxn."

6. k(T,P) values from partial networks don't always satisfy thermo consistence #58Py closed and reopened several times - related to barrier height vs activation energy and the ILT method: resolve by 1) making sure new rate rules have Ea that is close to Eo Invalid cantherm/measure input file created (multiple reactions with same label) #112Py - should be an easy fix measure.py vs cantherm.py #120Py - still? -> remove all usage of measure, if not done already. Enoch looking into ILT, however, common scenarios that guarantee inaccurate rates: 1.No k  available and E a estimated from thermo families (  Hrxn) 2.n > 2 for 3-parameter Arrhenius expressions in rate rules 3.At low T, rate rule incorporates large tunneling corrections 3. Pdep and invalid/inaccurate MCRCs

7. Extrapolation beyond T, P ranges => Solver failure Rate used in RMG-Py outside of specified temperature in input file #55Py RWest asked WWJD (what would java do?) …crickets answered. Similar issues elsewhere, #67Py extrapolating P-dep rates outside recommended range of P #67Py, which can cause DDASSL to fail errors associated with #67 not saved to log #68Py in general, this is a small issue when chemistry and thermo are reasonable

8. 4. QM(TP) Extra QM data not used in PDep calculations #133Py QM calculations don't check correct molecule is found#136Py Beat’s new adjacency list, although little data for new possible electronic states Unclear how this will pan out: unforeseen scenarios, potential for memory/speed issues May have to be dealt with on a case-by-case basis 5. Many Multiplicity Issues

9. Propene + O( 3 P): over 40% of the product total product (4 torr, 298 K) yield may require ISC from the triplet to the lower-lying singlet Savee et al. (Taatjes) 2012 PCCP propene + O [CH2]C(C)[O] C[CH]C[O] [CH2]C=C + [OH] C=[C]C + [OH] CC1CO1 RMG-Py Exact match found for rate rule (o_atom,mb_db) GenerateReactions:

10. + OH Biradicals – 1,3-butadiene + O( 3 P) via GenerateReactions + O( 3 P) Exact match found for rate rule (o_atom,mb_db)

11. Biradicals – benzene + O( 3 P) Taatjes et al. 2010 JPCA Note: phenoxy + OH product not shown

12. 6. Documentation requests for more documentation comments about incorrect documentation Resolution: when you make a commit, try to check the documentation and see if there's anything related to your commit. If not, spend the extra few minutes to add to the documentation Example input files need updating #122 More examples and documentation #66

13. General reminders See Connie’s presentation on Git/Sphinx basics (9.20.2013) – adhere to general policies (best business practices) When adding nodes/reactions, add intermediate levels and not just the detailed one. Be sure to include valid T, P ranges, uncertainties if available, and source. Quality control – never too busy for it All of this requires more work on our part, but it’s worth it in the end, right?

14. Other [more general] Issues from previous meetings: RMG’s fast-paced evolution makes it difficult for general public to use. Solution: a stable release? Once we accomplish x (e.g., database, nitrogen chemistry, ILT issues resolved), release a frozen version to the world with list of cases where we know it works? Py vs. Java war – the new Israel-Palestine conflict?

15. Biradicals – addendum to Beat’s talk