simulator.engines¶

The executor of the engine of a model.

execute_plan runs a plan on a loaded model with the executor of its engine: sbmlsim.simulator.executor for roadrunner, sbmlsim.simulator.executor_copasi for COPASI and sbmlsim.simulator.executor_amici for AMICI, which are imported when a model of their engine runs, so a run of roadrunner never imports COPASI or AMICI. Every simulation of the package outside the executors runs through it: the simulator, the workers of a scan and the evaluation of a fit.

execute_plan ¶

execute_plan(plan, model, selections)

Run a plan on a loaded model with the executor of its engine.

Parameters:

Name	Type	Description	Default
`plan`	`Plan`	the plan, compiled against the model.	required
`model`	`SBMLModel`	the loaded model, of roadrunner, COPASI or AMICI.	required
`selections`	`Sequence[str]`	the columns of the output, the time first.	required

Returns:

Type	Description
`TimecourseResult`	The output of the simulation.

Raises:

Type	Description
`RuntimeError`	if the engine fails to integrate.
`SteadyStateError`	if a presimulation finds no steady state.
`NotImplementedError`	for a feature the engine does not simulate, the same for every plan of the model, see `check_plan`.
`TypeError`	if the model is not a model of its engine.
`ValueError`	for an engine without an executor.

check_plan ¶

check_plan(plan, model)

Check that the engine of a model simulates a plan, before it runs.

A feature the engine does not simulate is the same for every point of a plan, so a run checks it once before it runs a point, serially or in a pool; the executor checks every plan as well. roadrunner simulates every plan, COPASI refuses a change of a conversion factor and a delayed event of the model in a plan which sets values between two runs, see sbmlsim.simulator.executor_copasi.check_supported, and AMICI a change of a compartment it keeps out of its states, see sbmlsim.simulator.executor_amici.check_supported.

Parameters:

Name	Type	Description	Default
`plan`	`Plan`	the plan, compiled against the model, with the values of a point.	required
`model`	`SBMLModel`	the loaded model.	required

Raises:

Type	Description
`NotImplementedError`	for a feature the engine does not simulate.
`TypeError`	if the model is not a model of its engine.
`ValueError`	for an engine without an executor.