scine_chemoton.gears.kinetic_modeling.kinetic_modeling¶
Classes
This gear sets up kinetic modeling jobs as soon as no other jobs are pending/waiting. |
- class scine_chemoton.gears.kinetic_modeling.kinetic_modeling.KineticModeling[source]¶
This gear sets up kinetic modeling jobs as soon as no other jobs are pending/waiting.
- Attributes:
- optionsKineticModeling.Options
The options for the KineticModeling gear.
- class Options[source]¶
The options for the KineticModeling Gear.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
- energy_reference_type¶
- str
The energy reference type. zero -> absolute energies are used. atom -> Atomization energies are used.
-
energy_references:
MultiModelEnergyReferences¶ - MultiModelEnergyReferences
Optional atom energy calculators for each model combination. If none are provided, they are constructed on the fly.
-
flux_variance_label:
str¶ - str
If not empty, the minimum flux truncation also considers the flux’s variance.
- job¶
- int
Set up a kinetic modeling job if at least this number of new elementary steps were added to the network and are eligible according to reaction-barrier cutoff, and electronic structure model.
- job_settings¶
- ValueCollection
The job settings. See get_default_settings(job) for default settings.
-
min_flux_truncation:
float¶ - float
Minimum flux of all aggregates in a reaction in a previous kinetic modeling job. If the flux is lower than this threshold, the reaction is excluded from the kinetic modeling.
-
model:
Model¶ - db.Model
The model the Gear is working with.
-
model_combinations:
List[ModelCombination]¶ - List[ModelCombinations]
The hierarchy of model combinations
- model_combinations_reactions¶
- List[ModelCombinations]
The hierarchy of model combinations for reaction barriers.
- only_electronic¶
- bool
If true, only the electronic energies are used for the rate constant calculations.
-
reference_state:
ReferenceState¶ - ReferenceState
The thermodynamic reference state defined by temperature (in K) and pressure (in Pa).
-
uncertainty_estimator:
UncertaintyEstimator¶ - UncertaintyEstimator
The uncertainty estimator for the thermodynamic parameters (only used in RMS kinetic modeling).
-
cycle_time: