Micki v2.2.0

Reactions as strings

Reactions can now be written as strings of species labels, which is the recommended form:

reactions = micki.reactions_from_strings(sp, {
    'co_ads': ('co_g + * -> co', {'method': 'STICK'}),
    'o2_ads': 'o2_g + 2* <-> o-o -> 2 o',
    'co_ox': 'co + o <-> o-co -> co2_g + 2*',
})

• Reaction.from_string(expression, species, **kwargs) reads 'reactants -> products' or CatMap's 'reactants <-> ts -> products' (-> and <-> are interchangeable; steps stay reversible unless reversible=False).
• Coefficients: 2 h, 2*h or 2h. * is the empty site when there is a single site type, whatever its label.
• species is a dict (e.g. from read_from_db) or a list. A dict can also map CatMap names such as '*_s' to micki species.
• micki.reactions_from_strings builds a whole mechanism for Model.add_reactions.
• The species-object form, Reaction(reactants, products, ts=...), works as before.

New checks (may raise errors in existing scripts)

• Atom balance: every Reaction checks that its reactants, products and transition state contain the same atoms. Empty sites and electrons are not counted, and an adsorbate's slab atoms are subtracted. Pass check_balance=False for deliberately unbalanced steps.
• Sites: Model.set_initial_conditions raises an error for an adsorbate that occupies no sites and is not itself an empty site (usually a forgotten sites=), and, with a lattice, for a transition state without sites. Mark species that deliberately occupy no sites (e.g. mobile precursors) with Adsorbate(..., sitefree=True); this is stored in databases.

The water-gas shift model and the CatMap comparison models pass both checks unchanged.

Examples and documentation

• examples/wgs.py: the water-gas shift model written with reaction strings, runnable from a clone (python examples/wgs.py), printing TOFs against experiment. A test checks that it matches the regression model.
• The docs lead with reaction strings. The user guide's example explains its made-up energies and shows how species come from VASP output or an ASE calculator.

Micki v2.1.0

Added documentation and CatMap compatibility mode.

Micki v2.0.1

Release 2.0.1

No code changes since 2.0.0. Publishes the README that recommends
installing with pip on PyPI, and is the first release with the publish
workflow on Node 24 actions.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Micki v2.0.0

Micki v2.0.0, now using the Sundials Python interface.