atomica.model.Link

class atomica.model.Link(pop, parameter, source, dest)

Bases: Variable

A Link is a Variable that maps to a transition between compartments. As such, it contains an inflow and outflow compartment. A Link’s value is generally derived from a Parameter, and there may be multiple links that draw values from the same parameter. The value corresponds to the number transferred from the source compartment to the destination compartment in the subsequent timestep.

Some links do not have an associated Parameter object because their values are calculated by means other than parameters. For example

• Flush links have their values calculated from the source timed compartment

• Junction residual links have their values calculated by junction balancing

Attributes

name	Variable code name
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

create	Create and wire up a new link
plot	Produce a time series plot
preallocate	Preallocate data storage
relink
set_dynamic	Make the variable a dependency
unlink
update	Update the value of the link

classmethod create(pop, parameter, source, dest)

Create and wire up a new link

This method instantiates a Link (including of derived types) and also wires it up to the population, parameter, source, and destination compartments. This allows the Link constructor to be used without needing the entire population infrastructure

Parameters:

• pop – A Population instance that will contain the new Link

• parameter – A Parameter instance that will supply values for the new Link

• source – A Compartment instance to transfer from

• dest – A Compartment instance to transfer to

Returns:

The newly created Link instance

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

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

pop

Reference back to the Population containing this object

preallocate(tvec, dt)

Preallocate data storage

This method gets called just before integration, once the final sizes of the arrays are known. Performance is improved by preallocating the arrays. The tvec attribute is assigned as-is, so it is typically a reference to the array stored in the parent Model object. Thus, there is no duplication of storage there, and Variable.tvec is mainly for convenience when interpolating or plotting.

This method may be overloaded in derived classes to preallocate other variables specific to those classes.

Parameters:

• tvec (array) – An array of time values

• dt (float) – Time step size

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, converted_frac)

Update the value of the link

This method takes in the fraction of the source compartment to move, and updates the value of the link accordingly. In update_links, parameters are first all converted into timestep-based fractions. These fractions are then used to update the links. However, depending on whether the link stores compartment duration information, this update may or may not require the use of TimedCompartment properties. Therefore, updating the link is delegated to this Link method that can be overloaded in derived classes.

Parameters:

• ti (int) – The time index to update

• converted_frac (float) – The fraction of the source compartment to move (the parent parameter value, converted to timestep fraction)

Return type:

None