atomica.model.SinkCompartment

class atomica.model.SinkCompartment(pop, name)

Bases: Compartment

Attributes

name	Variable code name
outflow	Return the outflow at all times
id	Unique identifier for the integration object
units	The units for the quantity, used for plotting and for validation.
pop	Reference back to the Population containing this object

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)

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.

Returns:

A code name

property outflow: array

Return the outflow at all times

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)

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)

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)

Update sink compartment value

A sink compartment has inputs only

Parameters:

ti (int) – Time index to update

Return type:

None