KPP to MICM #173
Merged
KPP to MICM #173
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportPatch and project coverage have no change.
Additional details and impacted files@@ Coverage Diff @@
## main #173 +/- ##
=======================================
Coverage 96.80% 96.80%
=======================================
Files 24 24
Lines 1974 1974
=======================================
Hits 1911 1911
Misses 63 63 ☔ View full report in Codecov by Sentry. |
mattldawson
approved these changes
Aug 3, 2023
K20shores
requested changes
Aug 4, 2023
etc/scripts/kpp_to_micm.py
Outdated
| for reactant in reactants: | ||
| if reactant[0].isdigit(): | ||
| equation_dict['reactants'][reactant[1:]] \ | ||
| = {'yield': float(reactant[0])} |
There was a problem hiding this comment.
Suggested change
| = {'yield': float(reactant[0])} | |
| = {'qty': float(reactant[0])} |
I believe the stoichiometric coefficient on the reactants side is called the quantity, abbreviated to qty, in the configuration format we use.
etc/scripts/kpp_to_micm.py
Outdated
Comment on lines
211
to
216
| parser.add_argument('--micm_species', type=str, | ||
| default=os.path.join('..', 'configs', 'micm', 'species.json'), | ||
| help='MICM output species config file') | ||
| parser.add_argument('--micm_reactions', type=str, | ||
| default=os.path.join('..', 'configs', 'micm', 'reactions.json'), | ||
| help='MICM output reactions config file') |
There was a problem hiding this comment.
Would it be possible to change the default output directory to the name of the mechanism, maybe a path of ../configs/micm/<mechanism>? At least this way any overwrite would be for the same mechanism
boulderdaze
approved these changes
Aug 4, 2023
K20shores
approved these changes
Aug 4, 2023
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR for initial implementation.
Need still to test MICM with the generated JSON from the KPP Chapman example ...
Description:
kpp_to_micm.py translates KPP config files to MICM JSON config files
(desginated by the suffixes .kpp, .spc, .eqn, .def)
from a single directory specified by the --kpp_dir argument.
TODO:
(1) Parse both A and B Arrhenius coefficients from KPP equations
Currently a single rate coeffient is assigned to A and B is set to 0.
(2) Translate stoichiometric coefficients in the equation string
with more than one digit.
(3) Add method unit tests with pytest.
(4) Add support for many more reaction types ...