Adding a built-in model#

Built-in models ship as YAML files under aquakin/models/. Adding one:

  1. Author the YAML file. See the Model file format for the schema and aquakin/models/ozone_bromate.yaml for a worked example.

  2. Verify it loads:

    import aquakin
net = aquakin.load_model("my_model")
print(net.summary())

  3. Add a unit-test fixture covering the new model’s structural assertions (species count, stoichiometry of key reactions).

  4. If experimental trajectories are available, add a validation test under tests/validation/ decorated with @pytest.mark.validation.

  5. List the new model in the README and the Model catalog.

Authoring tips#

  • Lead with description: and references: blocks. Future contributors will thank you.

  • Every reaction should carry a reference: line citing the rate-constant source.

  • For acid/base speciation, use pH_switch(pKa) rather than baking pH into rate constants. Keeps the model usable across pH ranges.

  • For temperature-dependent rates, use arrhenius(A, Ea) so that the model works at any T declared as a condition.

  • Use bounds: on parameters when ranges are known from the literature. aquakin.fit will respect them as box constraints.