amici.amici.SimulationParameters

class amici.amici.SimulationParameters(*args)[source]

Container for various simulation parameters.

__init__(*args)[source]

Overload 1:

Constructor

Parameters

timepoints (DoubleVector) – Timepoints for which simulation results are requested


Overload 2:

Constructor

Parameters

Overload 3:

Constructor

Parameters
  • fixedParameters (DoubleVector) – Model constants

  • parameters (DoubleVector) – Model parameters

  • plist (IntVector) – Model parameter indices w.r.t. which sensitivities are to be computed


Overload 4:

Constructor

Parameters
  • timepoints (DoubleVector) – Timepoints for which simulation results are requested

  • fixedParameters (DoubleVector) – Model constants

  • parameters (DoubleVector) – Model parameters

Methods Summary

__init__(*args)

Overload 1:

reinitializeAllFixedParameterDependentInitialStates(…)

Set reinitialization of all states based on model constants for all simulation phases.

reinitializeAllFixedParameterDependentInitialStatesForPresimulation(…)

Set reinitialization of all states based on model constants for presimulation (only meaningful if preequilibration is performed).

reinitializeAllFixedParameterDependentInitialStatesForSimulation(…)

Set reinitialization of all states based on model constants for the ‘main’ simulation (only meaningful if presimulation or preequilibration is performed).

Attributes

fixedParameters

Model constants

fixedParametersPreequilibration

Model constants for pre-equilibration

fixedParametersPresimulation

Model constants for pre-simulation

parameters

Model parameters

plist

Parameter indices w.r.t.

pscale

Parameter scales

reinitialization_state_idxs_presim

Indices of states to be reinitialized based on provided presimulation constants / fixed parameters.

reinitialization_state_idxs_sim

Indices of states to be reinitialized based on provided constants / fixed parameters.

reinitializeFixedParameterInitialStates

Flag indicating whether reinitialization of states depending on fixed parameters is activated

sx0

Initial state sensitivities

t_presim

Duration of pre-simulation.

ts_

Timepoints for which model state/outputs/.

tstart_

starting time

x0

Initial state

Methods

__init__(*args)[source]

Overload 1:

Constructor

Parameters

timepoints (DoubleVector) – Timepoints for which simulation results are requested


Overload 2:

Constructor

Parameters

Overload 3:

Constructor

Parameters
  • fixedParameters (DoubleVector) – Model constants

  • parameters (DoubleVector) – Model parameters

  • plist (IntVector) – Model parameter indices w.r.t. which sensitivities are to be computed


Overload 4:

Constructor

Parameters
  • timepoints (DoubleVector) – Timepoints for which simulation results are requested

  • fixedParameters (DoubleVector) – Model constants

  • parameters (DoubleVector) – Model parameters

reinitializeAllFixedParameterDependentInitialStates(nx_rdata: int)None[source]

Set reinitialization of all states based on model constants for all simulation phases.

Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim

Parameters

nx_rdata (int) – Number of states (Model::nx_rdata)

Return type

None

reinitializeAllFixedParameterDependentInitialStatesForPresimulation(nx_rdata: int)None[source]

Set reinitialization of all states based on model constants for presimulation (only meaningful if preequilibration is performed).

Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim

Parameters

nx_rdata (int) – Number of states (Model::nx_rdata)

Return type

None

reinitializeAllFixedParameterDependentInitialStatesForSimulation(nx_rdata: int)None[source]

Set reinitialization of all states based on model constants for the ‘main’ simulation (only meaningful if presimulation or preequilibration is performed).

Convenience function to populate reinitialization_state_idxs_presim and reinitialization_state_idxs_sim

Parameters

nx_rdata (int) – Number of states (Model::nx_rdata)

Return type

None