RMG Study Group/Meeting – Summary of the many Github issues and [hopefully] ways to resolve them

March 14, 2014Enoch Dames

Note: Will someone please log notes from this meeting?

232 unresolved issues on GithubRMG-Py: 90RMG-Java: 91 (some relevance to Py)RMG-Database: 14 Resolutions in progress with the Universal DatabaseRMG-website: 37Many similar issues and themes have been repeated over the last 4 years:

1. Symmetry and reaction path degeneracy2. Aromaticity and Resonance3. Pdep: failing solvers, invalid MCRCs4. QM(TP)5. Multiplicity6. Documentation issues

The good news: • the most pressing issues are already being addressed! • some of these issues may already be fixed, but remain open

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

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

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."

• 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 Ea estimated from thermo families (Hrxn)

2. n > 2 for 3-parameter Arrhenius expressions in rate rules3. At low T, rate rule incorporates large tunneling corrections

3. Pdep and invalid/inaccurate MCRCs

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

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

Propene + O(3P): 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 RMG-Py

RMG-Py

Exact match found for rate rule (o_atom,mb_db)

GenerateReactions:

+ OH

+ OH

Biradicals – 1,3-butadiene + O(3P) via GenerateReactions

+ O(3P)

Exact match found for rate rule (o_atom,mb_db)

Biradicals – benzene + O(3P)Re

lativ

e En

ergy

( kc

al /

mol

)

20

+ O ( 3P)

+ CO

HO

ISC

0

–20

–40

–60

–80

–100

3 A’, 1A’, 3A”, 1A”within 8 kcal/mol

+ H

O

OO

C

O

OO

O

OH

+ HCO

+ H+CO

Rela

tive

Ener

gy (

kcal

/ m

ol )

20

+ O ( 3P)

+ CO

HO HO

ISC

0

–20

–40

–60

–80

–100

3 A’, 1A’, 3A”, 1A”within 8 kcal/mol

+ H

O

OOOO

C

O

C

O

OOOO

O

OHOH

+ HCO

+ H+CO

Taatjes et al. 2010 JPCA

Note: phenoxy + OH product not shown

6. Documentation

• requests for more documentation• comments about incorrect documentationResolution: 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

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?

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?

0.0

0.2

0.4

0.6

0.8

1.0 0.1

1

10

100400

600800

1000 12001400

1600 18002000

Bra

nchi

ng R

atio

0.0

0.2

0.4

0.6

0.8

1.0 0.1

1

10

100400

600800

1000 12001400

1600 18002000

0.0

0.2

0.4

0.6

0.8

1.0 0.1

1

10

100400

600800

1000 12001400

1600 18002000

0.0

0.2

0.4

0.6

0.8

1.0 0.1

1

10

100400

600 8001000

12001400 1600

18002000

Bra

nchi

ng R

atio

0.0

0.2

0.4

0.6

0.8

1.0 0.1

1

10

100400

600 8001000

12001400 1600

18002000

0.0

0.2

0.4

0.6

0.8

1.0 0.1

1

10

100400

600 8001000

12001400 1600

18002000

Biradicals – addendum to Beat’s talk