Yaml writer addition - #2800

Merged

rwest merged 100 commits into

mainfrom

yaml_writer_addition

May 8, 2026

Commits on May 8, 2026

Save cantera files that were made from chemkin files to a separate folder.
rwest
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486cdfa
Rename yml to yaml_rms, because it was specific to RMS

Nora-Khalil
authored and
rwest
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a6ad29d
Enable Cantera-YAML writing.

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8f560f6
Reworking the Elements blocks in cantera yaml writer.
rwest
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78e9124
add yaml writer test to compare yaml file generated by RMG and the yaml file converted from chemkin files

Lekia Prosper
authored and
rwest
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f5757ec
Simplify species_to_dict for writing cantera yaml.
rwest
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d14c6e2
Rename generate_cantera_files to generate_cantera_files_from_chemkin
rwest
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676ff56
Add (or restore?) a TestCanteraOutputConversion test
rwest
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c30e394
Functional test comparing Cantera YAML outputs to Chemkin-converted YAML
rwest
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8f6a48b
YAML: Reaction comparison can do irreversible reactions
rwest
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5fb4569
Enhance reaction comparison by adding checks for reaction counts and conditional comparison of Arrhenius parameters
rwest
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f9c0d47
Simplify CompareYaml and YamlAnalyst arguments
rwest
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a05dc08
Move test_make_cantera_input_file into ..._from_ck and make a ..._directly
rwest
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21bf695
Tweak test_yaml
rwest
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d9da484
Update test_yaml.py to use new YAML test files for comparison
rwest
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2b032e9
A stub cantera_yamlTest.py file for testing the cantera yaml features.
rwest
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50cdee9
Work on the yaml_canteraTest.
rwest
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a07a051
Work on yaml_canteraTest.py. Check phases.
rwest
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69a511e
TEMP? mainTest functional test now copies the yaml files into the test folder.
rwest
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6aee997
[yaml_cantera] Make phase names mach ck2yaml version.
rwest
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0f1180c
[yaml_cantera] Fix where transport data comments are put
rwest
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e803c06
[yaml_canteraTest] More testing of phase definitions.
rwest
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2a1bb13
[yaml_canteraTest] Test the Elements block
rwest
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044b1d0
[yaml_cantera] Outputs more condensed, with flow_style for some lists.
rwest
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de07328
Update the cantera yaml test data files.
rwest
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e36c015
[yaml_cantera] Add test for species definition matching.
rwest
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a20e68e
[yaml_canteraTest] fix species test for NASA polynomial collapse.
rwest
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e482a09
Converted cantera SI units to the units specified in write_cantera

LekiaAnonim
authored and
rwest
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0d200f6
yaml comparer: Added a normalization method for equation with third-body.

LekiaAnonim
authored and
rwest
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2a42a14
yaml comparer: use cantera to compare rate

LekiaAnonim
authored and
rwest
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286e287
Fix YAML serialization of Cantera objects by converting AnyMap to dict
rwest
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265e5d3
TEMP? Newly created yaml files for testing.
rwest
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a6e5f98
Enhance compare_yaml_outputs
rwest
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96c8b20
yaml_canteraTest compares yaml files made in mainTest
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b00bdc5
Making a new tool compare_cantera_yaml
rwest
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9bc667d
Refactor Cantera YAML comparison tool with enhanced features
rwest
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2ccd0be
The compare_cantera_yaml script now uses logging.
rwest
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70d8ff1
At end of model generation, compare direct yaml and ck2yaml outputs.
rwest
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168ea0d
Added a Cantera writer module

alongd
authored and
rwest
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8de144e
Move Alon's cantera writer to yaml_cantera2
rwest
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a1d1e3d
Rename Alon's CanteraWriter class to CanteraWriter2
rwest
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5d0060c
Tests: Cantera writer

alongd
authored and
rwest
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a93bcc1
Rename (file and contents) Alon's yaml_cantera2Test
rwest
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6f464a1
Add surface chemistry support to Cantera YAML export

alongd
authored and
rwest
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92b2a02
Updates output subdirectory name to 'cantera2'
rwest
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90defd8
[yaml_cantera] makes a copy of the latest chem.yaml each iteration
rwest
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3e01182
Attach the CanteraWriter2
rwest
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d50e15b
compare_cantera_yaml copes with different reaction block specification
rwest
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d9fdd43
Correct units for transport properties in CanteraWriter2
rwest
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fdad8b2
Fix transport properties in CanteraWriter2
rwest
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54e9f1b
[CanteraWriter2] Write transport and thermo notes where they belong.
rwest
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1aaf238
[CanteraWriter2] fix conversion of dipole monte into Debye
rwest
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19a5692
Fix attempt for 'E' in atom dictionary

alongd
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rwest
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a1307b5
Revert "Fix attempt for 'E' in atom dictionary"
rwest
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6d5820a
[yaml_cantera2] Fixing 'E' electron count for charged species.
rwest
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2d5cfda
Rename 'yaml_cantera' to 'yaml_cantera1'.
rwest
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2be92ea
[RMG/main] get_git_commit now returns strings not bytes
rwest
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aa46216
[yaml_cantera2] Detailed logging of the yaml generator
rwest
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8598065
[yaml_cantera1] Detailed logging of the yaml generator
rwest
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5f1c8a3
Revert "Converted cantera SI units to the units specified in write_cantera"
rwest
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4c87a1b
[yaml_cantera1] Report things in cantera default internal units.
rwest
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1051a90
[yaml_cantera1] Add coverage-dependent thermo to CanteraWriter1

rwest
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claude
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1c4790a
[yaml_cantera2] Add coverage-dependent thermo to CanteraWriter2

rwest
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claude
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2d0fbbb
Move coverage-dependent thermo into Species.to_cantera()

rwest
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claude
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0192058
[yaml_cantera2] use label if it's a Species (should save time)
rwest
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a7c2550
[yaml_cantera2] write species list in order of index
rwest
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5fb9f49
[yaml_cantera2] fix unit test (detecting the generator field)
rwest
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ff3a327
Fix PDepArrhenius.set_cantera_kinetics for duplicate-pressure PLOG
rwest
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20f9a7e
[yaml_cantera2] Unbox numpy P scalars in PDepArrhenius rate-constants

rwest
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claude
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ccb9b3a
[yaml_cantera2] Emit duplicate-pressure PLOG as one reaction, not split duplicates

rwest
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claude
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049959d
[yaml_cantera1] Add verboseComments support

rwest
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claude
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5e0a7d9
[yaml_cantera2] Add verboseComments support

rwest
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claude
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c8bca8e
[yaml_cantera1] Add saveEdgeSpecies support

rwest
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claude
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3ddf22d
[yaml_cantera2] cov_params is a dict with keys not a structure with attributes.

rwest
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djlucey
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d539f8f
[yaml_cantera1] Add coverage dependent kinetics.
rwest
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8da2b35
[yaml_cantera1] Move the coverage-dependence code into to_cantera
rwest
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73f8e35
Fixes to coverage-dependent kinetics. [requires rebuild of cython]
rwest
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c69f357
[yaml_cantera1] Add unit tests for species_to_dict and reaction_to_dicts

rwest
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claude
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c0a88a2
[yaml_cantera2] Add unit tests for surface species and reactions

rwest
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claude
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0ced931
Use CDumper (C-accelerated) in both Cantera YAML writers for faster output

rwest
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claude
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c568049
Use CDumper (C-accelerated) in RMS YAML writer for faster output

rwest
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claude
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4d3b2b6
Remove outdated Cantera files from testing directory.
rwest
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3237e3b
Add Cantera files from main test, to testing folder.
rwest
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1f40ed9
mainTest creates Cantera yaml files for testing.
rwest
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72a2bda
Add WriterConfig: per-writer output configuration data class

rwest
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claude
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bb4b2ab
Replaced cantera1 yaml test file with the verbose annotated one
rwest
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a1ee9fb
Parse per-writer configs from input files; store on RMG object

rwest
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claude
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fb0d161
fixup! Add Cantera files from main test, to testing folder.
rwest
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bc3f967
Wire WriterConfig into register_listeners() and all output writers

rwest
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claude
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037cad1
Fix yaml_cantera1Test test (generator name)
rwest
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ab4d0a4
Docs, example input, and unit tests for per-writer output configuration

rwest
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claude
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06cafcb
Fix yaml_cantera2Test mock RMG object missing verbose_comments attribute.
rwest
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9f357cc
Guard end-of-run Cantera translation and comparison behind writer configs

rwest
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claude
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b796eb9
Demonstrate per-writer config in example inputs

rwest
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claude
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20fc705
Fix --walltime CLI precedence over input.py settings
rwest
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39593f9
Merge pull request #2945 to enhance output options
rwest
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4e0f5b0
Adding documentation for new output writers.
rwest
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5c364dc
Fix end-of-run Cantera translation: correct folder name and guard missing annotated files

rwest
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claude
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442213b
mainTest now turns on the Cantera YAML writers for testing.
rwest
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8ac28f6
Tweak iteration counting and seed saving.
rwest
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458bb3f