atomica.model.SinkCompartment¶

class atomica.model.SinkCompartment(pop, name)[source]¶

Bases: atomica.model.Compartment

Attributes

`name`	Variable code name
`outflow`	Return the outflow at all times

Methods

`connect`	Construct link out of sink compartment
`expected_duration`
`expected_outflow`
`plot`	Produce a time series plot
`preallocate`	Preallocate sink compartment
`relink`
`resolve_outflows`	Resolve sink outflows
`set_dynamic`	Make the variable a dependency
`unlink`
`update`	Update sink compartment value

connect(dest, par)[source]¶

Construct link out of sink compartment

This method raises an error because sinks cannot have outflows

Parameters

dest – A Compartment instance
par – The parameter that the Link will be associated with

Return type

None

id¶: Unique identifier for the integration object

property name: str¶

Variable code name

This is implemented as a property method because the id of the Variable is a tuple containing the population name and the variable code name, so this property method returns just the variable code name portion. That way, storage does not need to be duplicated.

Return type: str
Returns: A code name

property outflow: numpy.array¶

Return the outflow at all times

Return type: array
Returns: The sum of outgoing links at all time indices

plot()¶

Produce a time series plot

This is a quick function to make a basic line plot of this Variable. Mainly intended for debugging. Production-ready plots should be generated using the plotting library functions instead

Return type: None

pop¶: Reference back to the Population containing this object

preallocate(tvec, dt)[source]¶

Preallocate sink compartment

A sink compartment is initialized with 0.0 value at the initial timestep

Parameters

tvec (array) – Simulation time vector
dt (float) – Simulation time step

Return type

None

resolve_outflows(ti)[source]¶

Resolve sink outflows

There should not be any outflows, so this function immediately returns

Return type: None

set_dynamic(**kwargs)¶

Make the variable a dependency

For Compartments and Links, this does nothing. For Characteristics and Parameters, it will set the dynamic flag, but in addition, any validation constraints e.g. a Parameter that depends on Links cannot itself be dynamic, will be enforced.

This method generally must be overloaded in derived classes e.g. Parameter.set_dynamic()

Return type: None

units¶: The units for the quantity, used for plotting and for validation. Note that the default 'unknown' units are distinct to dimensionless units, which have value ''

update(ti)[source]¶

Update sink compartment value

A sink compartment has inputs only

Parameters: ti (int) – Time index to update
Return type: None