atomica.model.Model

class atomica.model.Model(settings, framework, parset, progset=None, program_instructions=None)

Bases: object

A class to wrap up multiple populations within model and handle cross-population transitions.

Attributes

t	Simulation time vector (this is a brand new instance from the settings.tvec property method)
dt	Simulation time step

Methods

build	Build the full model.
flush_junctions	Flush initialization values from junctions
get_pop	Allow model populations to be retrieved by name rather than index.
process	Run the full model.
relink	Replace IDs with references
unlink	Replace references with IDs
update_comps	Set the compartment values at self._t_index+1 based on the current values at self._t_index and the link values at self._t_index.
update_links	Update link values
update_pars	Update parameter values

build(parset)

Build the full model.

dt

Simulation time step

flush_junctions()

Flush initialization values from junctions

If junctions have been initialized with nonzero values as a mcv1 for initializing the downstream compartments, then the junctions need to be flushed into the downstream compartments at the start of the simulation. This is done using the .flush() method of the JunctionCompartment. The order of the loop is important if junctions flow into other junctions - this needs to be computed from the graph prior to calling this method (so that Model.junctions is in the correct order)

Return type:

None

get_pop(pop_name)

Allow model populations to be retrieved by name rather than index.

process()

Run the full model.

Return type:

None

relink()

Replace IDs with references

This is the reverse operation of Model.unlink() where IDs are replaced with object references.

Return type:

None

t

Simulation time vector (this is a brand new instance from the settings.tvec property method)

unlink()

Replace references with IDs

This method replaces all references with IDs so that there are no circular references that prevent pickling. This operation is reversed using Model.relink(). These get called automatically when pickling and unpickling.

Note that primary storage of the variables is in the population objects, so that is the one place where the variables remain in-scope.

Return type:

None

update_comps()

Set the compartment values at self._t_index+1 based on the current values at self._t_index and the link values at self._t_index. Values are updated by iterating over all outgoing links

Return type:

None

update_links()

Update link values

This method takes the current parameter values in the model, and uses them to populate associated links. This requires conversion between parameter units and actual flow rates.

Methods that populate links by means other than parameter e.g. Compartment.resolve_outflows or Junction.balance also get called here.

Return type:

None

update_pars()

Update parameter values

Run through all parameters and characteristics, updating as required. This takes place in stages :rtype: None

1. Characteristics that are dependencies of parameters are updated

2. Parameters are updated in dependency order

   1. The parameter function is evaluated

   2. The parameter is overwritten by programs

   3. The parameter is updated with the population aggregation calculation

   4. The parameter value is constrained

The parameters are updated parameter-at-a-time (across populations) so that the population aggregation can be carried out.

Only parameters that are required for transitions or that are overwritten by programs are modified here - otherwise, parameter values are computed in vector calculations either before integration (if the value is purely from the databook) or after integration (if the parameter depends on any flow rates or compartment sizes).