ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

Include BACs to obtain accurate k_rev

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Type: Feature
Dominant language
Python
Stars
51
Forks
25
Avg merge
4d 5h
Merged PRs (30d)
15

Description

Is your feature request related to a problem? Please describe.
When using ARC to run Arkane to obtain a rate constant, ARC currently has bac_type=None for all kinetics calculations so k_fwd is meaningful but the species thermo, Keq, and k_rev are not. This works well if the user wants to create a library of k_fwd before an RMG job. However, it may be useful to add an optional argument to indicate the direction and to include BACs; these would allow the other quantities present in rxns/ts/arkane/output.py to be meaningful.

Describe the solution you'd like
The default behavior should be preserved. Some optional features to consider are

  • call Arkane once without BACs and again (still without BACs) to generate another kinetic library of all the reverse rates. This would likely require the user to decide which library should be used and would only be helpful for small batches
  • call Arkane once without BACs to obtain an accurate k_fwd and again with BACs to obtain an accurate Keq that could be used to obtain an accurate k_rev. Something to keep in mind is that the reaction should be written in the direction that has the reactant and TS as most similar, which gives better cancellation of errors in the calculation of k_fwd. Typically, this means writing in the exothermic direction, but there are exceptions in which the endothermic direction better supports this goal, such as bond scission in a ring since the TS will be cyclic like the reactant

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in arc/processor.py at the kinetics calculation path around lines 107-147, then inspect rxns/ts/arkane/output.py for the thermo, Keq, and reverse-rate outputs. Define the optional BAC and direction behavior while preserving the current default; done should make the requested quantities meaningful without changing existing forward-rate workflows.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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