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simulator.changes

The changes of a plan and the events a change fires, independent of the engine.

An executor applies the changes of a plan at their times and fires the events of the model whose triggers a change made true (PEtab v2, reinitialization), which an engine does not see, since the values are set between two integrations. Both read and write the values of the model through ModelValues, the getValue/setValue of the selections of roadrunner, which roadrunner.RoadRunner has and an executor of another engine provides, see sbmlsim.simulator.executor.

ModelValues

Bases: Protocol

The current values of a model in the selections of roadrunner.

A selection is S for the amount of a species, [S] for its concentration, or the id of a parameter or a compartment. roadrunner.RoadRunner satisfies the protocol.

getValue 

getValue(selection)

Get the current value of a selection.

setValue 

setValue(selection, value)

Set the current value of a selection.

SBMLModelLike

Bases: Protocol

The model of the messages of the events.

Attributes:

Name Type Description
sid str | None

id of the model, None without one.
reported_triggers set[str]

the events whose trigger was reported as no math the simulator evaluates, so a trigger is reported once.

label property 

label

Get the name of the model in a message, see SBMLModel.label.

apply_changes 

apply_changes(event, values, plan)

Apply the assignments of a change.

Every value is evaluated first, with the state at the time of the change, then every target is set; a compartment keeps the concentration of the concentration species in it (PEtab v2).

Parameters:

Name Type Description Default
event PlanEvent

the assignments at one time.

 required
values ModelValues

the values of the model.

 required
plan Plan

the plan, whose symbols resolve the targets.

 required

Raises:

Type Description
ValueError

if an assignment has neither a value nor a formula.

triggers 

triggers(events, values, time, model)

Evaluate the triggers of the events, None for one which is not evaluated.

A trigger which is no math the simulator evaluates, one with rateOf or delay, see sbmlsim.sbml_math.compile_math, is not evaluated, so a change does not fire its event; it is reported once per event of a model instance, so once per worker of a pool, which loads its own instance.

Parameters:

Name Type Description Default
events Sequence[EventSymbols]

the events of the model.

 required
values ModelValues

the values of the model.

 required
time float

the time of the model.

 required
model SBMLModelLike

the model, for the messages.

 required

Returns:

Type Description
list[bool | None]

The value of every trigger.

fire_start_events 

fire_start_events(events, start, values, time, model)

Fire the events whose trigger is false before the time 0 and true at the start.

roadrunner fires them at the start in the initial state, with the events they trigger in the order of their priorities, before a change at the start; the executors of COPASI and AMICI fire them with this function, their engines get the triggers of such events true before the time 0, see sbmlsim.model.model_copasi and sbmlsim.model.model_amici.

Parameters:

Name Type Description Default
events Sequence[EventSymbols]

the events of the model.

 required
start Sequence[bool]

by the position of an event, whether its trigger is false before the time 0 (initialValue="false"), see the start_events of the models of COPASI and AMICI.

 required
values ModelValues

the values of the model, in its initial state.

 required
time float

the time of the start.

 required
model SBMLModelLike

the model, for the messages.

 required

Returns:

Type Description
list[int]

The events which fired, by their positions, see fire_events.

fire_events 

fire_events(
    events, before, values, time, model, after=None
)

Fire the events whose triggers a change made true.

An engine does not see a trigger which becomes true by a value which is set between two integrations, so the executor fires such events (PEtab v2, reinitialization: the events are applied after the changes): the events execute one at a time in priority order. Priorities and triggers are evaluated again after every event, and a nonpersistent pending event is cancelled if its trigger becomes false. Assignment values are captured at the trigger or evaluated at execution, as the event specifies. An event with a delay is reported and not fired, an event whose priority is no math the simulator evaluates is reported and fires with the priority 0, the one of an event without a priority, and an event whose trigger or assignments are no math the simulator evaluates is reported and not fired, see triggers. One event fires at most MAX_EXECUTIONS_PER_EVENT times, which stops events which trigger each other in a cycle.

Parameters:

Name Type Description Default
events Sequence[EventSymbols]

the events of the model.

 required
before list[bool | None]

the triggers before the change.

 required
values ModelValues

the values of the model, in the state after the change.

 required
time float

the time of the change.

 required
model SBMLModelLike

the model, for the messages.

 required
after Sequence[bool | None] | None

the triggers after the change, evaluated in the state after it for None; the triggers after an event are always evaluated. An executor gives the triggers right after the time of the change, see sbmlsim.simulator.executor_amici.

 None

Returns:

Type Description
list[int]

The events which fired, by their positions, in the order of their
list[int]

executions; an event which fired twice is listed twice.