scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling

Classes

RMSKineticModelingJobFactory(...[, ...])

A class that creates RMS kinetic modeling jobs.

class scine_chemoton.gears.kinetic_modeling.rms_kinetic_modeling.RMSKineticModelingJobFactory(model_combinations, model_combinations_reactions, manager, energy_references, uncertainty_estimator=<scine_chemoton.utilities.uncertainties.ZeroUncertainty object>, only_electronic=False)

A class that creates RMS kinetic modeling jobs.

assert_non_negative_barriers(enthalpies, entropies, ea, reaction_str_ids, aggregate_str_ids, temperature)

Assert that no forward or backward reaction barrier is negative.

create_kinetic_modeling_job(settings)

Create the kinetic modeling job.

Return type:

bool

Parameters:

settingsutils.ValueCollection

The job settings.

Returns:

bool

True if the calculation was set up. False, otherwise.

static get_default_settings()

Getter for the job’s default settings.

Returns:

Dict

The settings dictionary.

static get_job()

Getter for the db.Job object.

Returns:

db.Job

The object.

get_reactions()

The reactions are added iteratively starting from all compounds with a non-zero starting concentration. Reactions are added subject to the following conditions: 1. The barrier does not exceed max_barrier. 2. The reaction was not found to be negligible in a previous kinetic modeling run. 3. One site of the reaction can be reached through already added reactions or consists solely of starting aggregates.

Return type:

Tuple[Set[Reaction], Dict[int, Aggregate]]

static order_dependent_setting_keys()

Return type:

List[str]