write_yaml produces inconsistant reactions sections

[BangShiuh]

When the "reactions" in the cantera yaml input file contain multiple keys, the gas object will store the keys. However, when using write_yaml from the gas object, the output file only has the keys in the phases section.

Steps to reproduce

1. unzip test.zip
2. Run test.py

Behavior

InputFileError thrown by AnyMap::at: Error on line 1 of ./outfile.yaml: Key 'collisions' not found.

System information

• Cantera version: 3.0.0a4
• Python 3.11.3

Attachments

Additional context

test.zip

[ischoegl]

I'm not sure this is a bug. Cantera internally doesn't keep track of where reactions originated, so this behavior is expected (it writes out all reactions into a single field.

Presumably this is required for #1262? In case you indeed need a separate YAML collisions field, you'll have to incorporate an appropriate fix in your PR.

[speth]

Whether it's a bug to merge multiple reactions sections or not is debatable. But even if we do want to keep the current behavior of merging them, then the phase definition shouldn't reference the second, nonexistent section as demonstrated in this report.

[ischoegl]

@speth ... I did not catch that. For reference, this is the offending section in the serialized output

phases:
  - kinetics: gas
    name: discretized-electron-energy-plasma
    thermo: plasma
    elements: [O, E]
    species: [E, O2, O2-]
    electron-energy-distribution:
      type: discretized
      energy-levels: [0.0, 0.1, 1.0, 10.0]
      distribution: [0.0, 0.2, 0.7, 0.01]
      normalize: false
    state:
      T: 298.15
      density: 2.242267962000731e-05
      Y: {E: 1.0}
    reactions:
      - reactions: all
      - collisions: all

Whether it's a bug to merge multiple reactions sections or not is debatable.

... I think it's appropriate to merge.