Class SimulationParameters

Inheritance Relationships

Derived Type

Class Documentation

class amici::SimulationParameters

Container for various simulation parameters.

Subclassed by amici::ExpData

Public Functions

SimulationParameters() = default
SimulationParameters(std::vector<realtype> timepoints)

Constructor.

Parameters

  • timepoints: Timepoints for which simulation results are requested

SimulationParameters(std::vector<realtype> fixedParameters, std::vector<realtype> parameters)

Constructor.

Parameters

  • fixedParameters: Model constants

  • parameters: Model parameters

SimulationParameters(std::vector<realtype> fixedParameters, std::vector<realtype> parameters, std::vector<int> plist)

Constructor.

Parameters

  • fixedParameters: Model constants

  • parameters: Model parameters

  • plist: Model parameter indices w.r.t. which sensitivities are to be computed

SimulationParameters(std::vector<realtype> timepoints, std::vector<realtype> fixedParameters, std::vector<realtype> parameters)

Constructor.

Parameters

  • timepoints: Timepoints for which simulation results are requested

  • fixedParameters: Model constants

  • parameters: Model parameters

void reinitializeAllFixedParameterDependentInitialStatesForPresimulation(int nx_rdata)

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

void reinitializeAllFixedParameterDependentInitialStatesForSimulation(int nx_rdata)

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

void reinitializeAllFixedParameterDependentInitialStates(int nx_rdata)

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

Public Members

std::vector<realtype> fixedParameters

Model constants.

Vector of size Model::nk() or empty

std::vector<realtype> fixedParametersPreequilibration

Model constants for pre-equilibration.

Vector of size Model::nk() or empty. Overrides Solver::newton_preeq

std::vector<realtype> fixedParametersPresimulation

Model constants for pre-simulation.

Vector of size Model::nk() or empty.

std::vector<realtype> parameters

Model parameters.

Vector of size Model::np() or empty with parameter scaled according to SimulationParameter::pscale.

std::vector<realtype> x0

Initial state.

Vector of size Model::nx() or empty

std::vector<realtype> sx0

Initial state sensitivities.

Dimensions: Model::nx() * Model::nplist(), Model::nx() * ExpData::plist.size(), if ExpData::plist is not empty, or empty

std::vector<ParameterScaling> pscale

Parameter scales.

Vector of parameter scale of size Model::np(), indicating how/if each parameter is to be scaled.

std::vector<int> plist

Parameter indices w.r.t. which to compute sensitivities.

realtype tstart_ = {0.0}

starting time

realtype t_presim = {0.0}

Duration of pre-simulation.

If this is > 0, presimulation will be performed from (model->t0 - t_presim) to model->t0 using the fixedParameters in fixedParametersPresimulation

std::vector<realtype> ts_

Timepoints for which model state/outputs/… are requested.

Vector of timepoints.

bool reinitializeFixedParameterInitialStates = {false}

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

std::vector<int> reinitialization_state_idxs_presim

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

std::vector<int> reinitialization_state_idxs_sim

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