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ReactionMechanismGenerator / RMG-Py Public

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Yaml writer addition#2800

Merged

rwest merged 100 commits into

mainReactionMechanismGenerator/RMG-Py:mainfrom

yaml_writer_additionReactionMechanismGenerator/RMG-Py:yaml_writer_additionCopy head branch name to clipboard

May 8, 2026

Conversation Commits100 (100)Checks Files changed

Merged

Yaml writer addition#2800
rwest merged 100 commits into
mainfrom
yaml_writer_addition

Commits

Commits on May 8, 2026

Save cantera files that were made from chemkin files to a separate folder.
rwest
committed
Rename yml to yaml_rms, because it was specific to RMS

Nora-Khalil
authored and
rwest
committed
Enable Cantera-YAML writing.

committed
Reworking the Elements blocks in cantera yaml writer.
rwest
committed
add yaml writer test to compare yaml file generated by RMG and the yaml file converted from chemkin files

Lekia Prosper
authored and
rwest
committed
Simplify species_to_dict for writing cantera yaml.
rwest
committed
Rename generate_cantera_files to generate_cantera_files_from_chemkin
rwest
committed
Add (or restore?) a TestCanteraOutputConversion test
rwest
committed
Functional test comparing Cantera YAML outputs to Chemkin-converted YAML
rwest
committed
YAML: Reaction comparison can do irreversible reactions
rwest
committed
Enhance reaction comparison by adding checks for reaction counts and conditional comparison of Arrhenius parameters
rwest
committed
Simplify CompareYaml and YamlAnalyst arguments
rwest
committed
Move test_make_cantera_input_file into ..._from_ck and make a ..._directly
rwest
committed
Tweak test_yaml
rwest
committed
Update test_yaml.py to use new YAML test files for comparison
rwest
committed
A stub cantera_yamlTest.py file for testing the cantera yaml features.
rwest
committed
Work on the yaml_canteraTest.
rwest
committed
Work on yaml_canteraTest.py. Check phases.
rwest
committed
TEMP? mainTest functional test now copies the yaml files into the test folder.
rwest
committed
[yaml_cantera] Make phase names mach ck2yaml version.
rwest
committed
[yaml_cantera] Fix where transport data comments are put
rwest
committed
[yaml_canteraTest] More testing of phase definitions.
rwest
committed
[yaml_canteraTest] Test the Elements block
rwest
committed
[yaml_cantera] Outputs more condensed, with flow_style for some lists.
rwest
committed
Update the cantera yaml test data files.
rwest
committed
[yaml_cantera] Add test for species definition matching.
rwest
committed
[yaml_canteraTest] fix species test for NASA polynomial collapse.
rwest
committed
Converted cantera SI units to the units specified in write_cantera

LekiaAnonim
authored and
rwest
committed
yaml comparer: Added a normalization method for equation with third-body.

LekiaAnonim
authored and
rwest
committed
yaml comparer: use cantera to compare rate

LekiaAnonim
authored and
rwest
committed
Fix YAML serialization of Cantera objects by converting AnyMap to dict
rwest
committed
TEMP? Newly created yaml files for testing.
rwest
committed
Enhance compare_yaml_outputs
rwest
committed
yaml_canteraTest compares yaml files made in mainTest
rwest
committed
Making a new tool compare_cantera_yaml
rwest
committed
Refactor Cantera YAML comparison tool with enhanced features
rwest
committed
The compare_cantera_yaml script now uses logging.
rwest
committed
At end of model generation, compare direct yaml and ck2yaml outputs.
rwest
committed
Added a Cantera writer module

alongd
authored and
rwest
committed
Move Alon's cantera writer to yaml_cantera2
rwest
committed
Rename Alon's CanteraWriter class to CanteraWriter2
rwest
committed
Tests: Cantera writer

alongd
authored and
rwest
committed
Rename (file and contents) Alon's yaml_cantera2Test
rwest
committed
Add surface chemistry support to Cantera YAML export

alongd
authored and
rwest
committed
Updates output subdirectory name to 'cantera2'
rwest
committed
[yaml_cantera] makes a copy of the latest chem.yaml each iteration
rwest
committed
Attach the CanteraWriter2
rwest
committed
compare_cantera_yaml copes with different reaction block specification
rwest
committed
Correct units for transport properties in CanteraWriter2
rwest
committed
Fix transport properties in CanteraWriter2
rwest
committed
[CanteraWriter2] Write transport and thermo notes where they belong.
rwest
committed
[CanteraWriter2] fix conversion of dipole monte into Debye
rwest
committed
Fix attempt for 'E' in atom dictionary

alongd
authored and
rwest
committed
Revert "Fix attempt for 'E' in atom dictionary"
rwest
committed
[yaml_cantera2] Fixing 'E' electron count for charged species.
rwest
committed
Rename 'yaml_cantera' to 'yaml_cantera1'.
rwest
committed
[RMG/main] get_git_commit now returns strings not bytes
rwest
committed
[yaml_cantera2] Detailed logging of the yaml generator
rwest
committed
[yaml_cantera1] Detailed logging of the yaml generator
rwest
committed
Revert "Converted cantera SI units to the units specified in write_cantera"
rwest
committed
[yaml_cantera1] Report things in cantera default internal units.
rwest
committed
[yaml_cantera1] Add coverage-dependent thermo to CanteraWriter1

rwest
and
claude
committed
[yaml_cantera2] Add coverage-dependent thermo to CanteraWriter2

rwest
and
claude
committed
Move coverage-dependent thermo into Species.to_cantera()

rwest
and
claude
committed
[yaml_cantera2] use label if it's a Species (should save time)
rwest
committed
[yaml_cantera2] write species list in order of index
rwest
committed
[yaml_cantera2] fix unit test (detecting the generator field)
rwest
committed
Fix PDepArrhenius.set_cantera_kinetics for duplicate-pressure PLOG
rwest
committed
[yaml_cantera2] Unbox numpy P scalars in PDepArrhenius rate-constants

rwest
and
claude
committed
[yaml_cantera2] Emit duplicate-pressure PLOG as one reaction, not split duplicates

rwest
and
claude
committed
[yaml_cantera1] Add verboseComments support

rwest
and
claude
committed
[yaml_cantera2] Add verboseComments support

rwest
and
claude
committed
[yaml_cantera1] Add saveEdgeSpecies support

rwest
and
claude
committed
[yaml_cantera2] cov_params is a dict with keys not a structure with attributes.

rwest
and
djlucey
committed
[yaml_cantera1] Add coverage dependent kinetics.
rwest
committed
[yaml_cantera1] Move the coverage-dependence code into to_cantera
rwest
committed
Fixes to coverage-dependent kinetics. [requires rebuild of cython]
rwest
committed
[yaml_cantera1] Add unit tests for species_to_dict and reaction_to_dicts

rwest
and
claude
committed
[yaml_cantera2] Add unit tests for surface species and reactions

rwest
and
claude
committed
Use CDumper (C-accelerated) in both Cantera YAML writers for faster output

rwest
and
claude
committed
Use CDumper (C-accelerated) in RMS YAML writer for faster output

rwest
and
claude
committed
Remove outdated Cantera files from testing directory.
rwest
committed
Add Cantera files from main test, to testing folder.
rwest
committed
mainTest creates Cantera yaml files for testing.
rwest
committed
Add WriterConfig: per-writer output configuration data class

rwest
and
claude
committed
Replaced cantera1 yaml test file with the verbose annotated one
rwest
committed
Parse per-writer configs from input files; store on RMG object

rwest
and
claude
committed
fixup! Add Cantera files from main test, to testing folder.
rwest
committed
Wire WriterConfig into register_listeners() and all output writers

rwest
and
claude
committed
Fix yaml_cantera1Test test (generator name)
rwest
committed
Docs, example input, and unit tests for per-writer output configuration

rwest
and
claude
committed
Fix yaml_cantera2Test mock RMG object missing verbose_comments attribute.
rwest
committed
Guard end-of-run Cantera translation and comparison behind writer configs

rwest
and
claude
committed
Demonstrate per-writer config in example inputs

rwest
and
claude
committed
Fix --walltime CLI precedence over input.py settings
rwest
committed
Merge pull request #2945 to enhance output options
rwest
committed
Adding documentation for new output writers.
rwest
committed
Fix end-of-run Cantera translation: correct folder name and guard missing annotated files

rwest
and
claude
committed
mainTest now turns on the Cantera YAML writers for testing.
rwest
committed
Tweak iteration counting and seed saving.
rwest
committed

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