Aggregate

This is the class representing tightly organized molecular aggregates such as photosynthetic antenna and light-harvesting complexes in Quantarhei. Appart from represeting data, this class also provides a simplified interface to much of Quantarhei’s functionality, such as calculation of spectra and dynamics. In order to make the core more organized, the class Aggregate is the tip of series of mutually inheriting classes. They start with AggregateBase, a class which implements some of the core functionality and add functionality in classes like AggregateSpectroscopy, AggregateExcitonAnalysis etc.

Inheritance in Aggregate class

The dependency of the classes is the following

AggregateBase : basic functionality of the Aggregate

AggregateSpectroscopy : adds Liouville pathway generation

AggregateExcitonAnalysis : adds analysis of excitons

AggregatePureDephasing : adds calculation of effective pure dephasing rates

Aggregate : wraps everything up

Class Details

class quantarhei.builders.aggregates.Aggregate(molecules: list | None = None, name: str = '')

Bases: AggregatePureDephasing

Tightly organized molecular aggregate such as a photosynthetic antenna.

Combines a collection of Molecule objects into a coupled system and provides a unified interface for building Hamiltonians, computing spectra, and simulating dynamics. This class is the final layer in a hierarchy of inheriting classes that starts with AggregateBase.

Notes

Call build() after adding all molecules and setting all parameters before using any calculation methods.