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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?. 232 unresolved issues on Github. RMG- Py : 90 RMG-Java: 91 (some relevance to Py )

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rmg study group meeting summary of the many github issues and hopefully ways to resolve them

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?

232 unresolved issues on github
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:
  • Symmetry and reaction path degeneracy
  • Aromaticity and Resonance
  • Pdep: failing solvers, invalid MCRCs
  • QM(TP)
  • Multiplicity
  • 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
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 Pyand Java
2 aromaticity resonance
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
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."
slide6

3. Pdep and invalid/inaccurate MCRCs

  • 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:
  • No k available and Ea estimated from thermo families (Hrxn)
  • n > 2 for 3-parameter Arrhenius expressions in rate rules
  • At low T, rate rule incorporates large tunneling corrections
extrapolation beyond t p ranges solver failure
Extrapolation beyond T, P ranges => Solver failure
  • Rate used in RMG-Py outside of specified temperature in input file #55Py RWestasked 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
4. QM(TP)
  • Extra QM data not used in PDep calculations #133Py
  • QM calculations don't check correct molecule is found#136Py

5. Many MultiplicityIssues

  • 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
slide9

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

GenerateReactions:

propene + O <=> [CH2]C(C)[O]

<=> C[CH]C[O]

<=> [CH2]C=C + [OH]

<=> C=[C]C + [OH]

<=> CC1CO1

RMG-Py

RMG-Py

Exact match found for rate rule (o_atom,mb_db)

RMG-Py

Savee et al. (Taatjes) 2012 PCCP

slide10

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

+ OH

+ OH

  • + O(3P)

Exact match found for rate rule (o_atom,mb_db)

biradicals benzene o 3 p

+

H+CO

O

H

O

O

C

O

O

O

OH

Biradicals – benzene + O(3P)

A

A

,

,

A

A

,

,

A

A

,

,

A

A

3

3

1

1

3

3

1

1

within 8 kcal/mol

within 8 kcal/mol

20

20

+

H+CO

O

O

H

H

O

O

3

3

+ O (

+ O (

P)

P)

+

+

HCO

HCO

0

0

+ H

+ H

ISC

ISC

20

20

O

O

O

O

O

O

C

C

Relative Energy ( kcal / mol )

Relative Energy ( kcal / mol )

O

O

40

40

O

O

60

60

O

O

+ CO

+ CO

Taatjes et al. 2010 JPCA

OH

OH

80

80

100

100

Note: phenoxy + OH product not shown

6 documentation
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
general reminders
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
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?
  • Pyvs. Java war – the new Israel-Palestine conflict?