scine_chemoton.gears.kinetic_modeling.atomization

Classes

AtomEnergyReference(model, manager[, ...])	Reference the energy to the single atom energies to calculate energies of formation.
MultiModelEnergyReferences(references)	Energy references for a combination of electronic structure models.
PlaceHolderMultiModelEnergyReferences()	A place-holder for a MultiModelEnergyReferences object that can be used instead of None.
ZeroEnergyReference(model)	Default energy zero point of the electronic structure method.

class scine_chemoton.gears.kinetic_modeling.atomization.AtomEnergyReference(model, manager, atom_energies=None)

Reference the energy to the single atom energies to calculate energies of formation. You can calculate the energy of formation as energy - reference.get_reference_energy(structure_id).

get_atom_energy(element)

get_model()

Getter for the underlying model.

get_reference_energy(structure_id)

Getter for the electronic energy reference.

model_matches(model)

Return true, if the electronic structure models match.

set_up_atom_energy_calculations(reference_structure_ids)

Set up all atom energy calculations for the elements present in the given structures if these calculations where not already set up.

class scine_chemoton.gears.kinetic_modeling.atomization.MultiModelEnergyReferences(references)

Energy references for a combination of electronic structure models. The correct energy reference is determind on the fly for the given model. Energy references are only allowed once for every model.

get_energy_reference(model)

Getter for the electronic energy reference object with the given model.

get_value(aggregate)

Getter for the value of the electronic energy reference for the given aggregate wrapper.

Return type:

float

has_reference(model)

Returns true, if there is a fitting model.

class scine_chemoton.gears.kinetic_modeling.atomization.PlaceHolderMultiModelEnergyReferences

A place-holder for a MultiModelEnergyReferences object that can be used instead of None.

get_energy_reference(_)

Getter for the electronic energy reference object with the given model.

Return type:

float

get_value(_)

Getter for the value of the electronic energy reference for the given aggregate wrapper.

Return type:

float

has_reference(_)

Returns true, if there is a fitting model.

class scine_chemoton.gears.kinetic_modeling.atomization.ZeroEnergyReference(model)

Default energy zero point of the electronic structure method. The method is always taken without any solvent/ solvation settings.

get_model()

Getter for the underlying model.

get_reference_energy(_)

Getter for the electronic energy reference.

model_matches(model)

Return true, if the electronic structure models match.