atomica.model¶

Implements the Atomica computational graph

Fundamentally, models in Atomica can be represented as a graph, with nodes corresponding to compartments, and edges corresponding to transitions/links. This module implements the graph representation of the Framework in a form that can be numerically integrated. It also implements the methods to actually perform the integration.

Functions

run_model

Build and process model

Classes

`Characteristic`	A characteristic represents a grouping of compartments.
`Compartment`	A class to wrap up data for one compartment within a cascade network.
`JunctionCompartment`	A TimedCompartment has a duration group by virtue of having a .parameter attribute and a flush link.
`Link`	A Link is a Variable that maps to a transition between compartments.
`Model`	A class to wrap up multiple populations within model and handle cross-population transitions.
`Parameter`	Integration object to represent Parameters
`Population`	A class to wrap up data for one population within model.
`ResidualJunctionCompartment`	Junction with a residual outflow
`SinkCompartment`
`SourceCompartment`	Derived class for source compartments
`TimedCompartment`	Instantiate the TimedCompartment
`TimedLink`	A TimedLink connects two TimedCompartments
`Variable`	Integration object to manage compartments, characteristics, parameters, and links

Exceptions

`BadInitialization`	Error for invalid conditions
`ModelError`	Exception type for general model errors