Class SimulationParameters
Defined in File simulation_parameters.h
Inheritance Relationships
Derived Type
public amici::ExpData
(Class ExpData)
Class Documentation
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class amici::SimulationParameters
Container for various simulation parameters.
Subclassed by amici::ExpData
Public Functions
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SimulationParameters() = default
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inline explicit SimulationParameters(std::vector<realtype> timepoints)
Constructor.
- Parameters
timepoints – Timepoints for which simulation results are requested
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inline SimulationParameters(std::vector<realtype> fixedParameters, std::vector<realtype> parameters)
Constructor.
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inline SimulationParameters(std::vector<realtype> fixedParameters, std::vector<realtype> parameters, std::vector<int> plist)
Constructor.
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inline SimulationParameters(std::vector<realtype> timepoints, std::vector<realtype> fixedParameters, std::vector<realtype> parameters)
Constructor.
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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
andreinitialization_state_idxs_sim
- Parameters
nx_rdata – Number of states (Model::nx_rdata)
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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
andreinitialization_state_idxs_sim
- Parameters
nx_rdata – Number of states (Model::nx_rdata)
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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
andreinitialization_state_idxs_sim
- Parameters
nx_rdata – Number of states (Model::nx_rdata)
Public Members
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std::vector<realtype> fixedParameters
Model constants.
Vector of size Model::nk() or empty
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std::vector<realtype> fixedParametersPreequilibration
Model constants for pre-equilibration.
Vector of size Model::nk() or empty.
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std::vector<realtype> fixedParametersPresimulation
Model constants for pre-simulation.
Vector of size Model::nk() or empty.
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std::vector<realtype> parameters
Model parameters.
Vector of size Model::np() or empty with parameter scaled according to SimulationParameter::pscale.
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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
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std::vector<ParameterScaling> pscale
Parameter scales.
Vector of parameter scale of size Model::np(), indicating how/if each parameter is to be scaled.
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std::vector<int> plist
Parameter indices w.r.t. which to compute sensitivities.
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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
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std::vector<realtype> ts_
Timepoints for which model state/outputs/… are requested.
Vector of timepoints.
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bool reinitializeFixedParameterInitialStates = {false}
Flag indicating whether reinitialization of states depending on fixed parameters is activated.
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std::vector<int> reinitialization_state_idxs_presim
Indices of states to be reinitialized based on provided presimulation constants / fixed parameters.
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std::vector<int> reinitialization_state_idxs_sim
Indices of states to be reinitialized based on provided constants / fixed parameters.
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SimulationParameters() = default