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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SimulationParameters
(std::vector<realtype> timepoints)¶ Constructor.
- Parameters
timepoints
: Timepoints for which simulation results are requested
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SimulationParameters
(std::vector<realtype> fixedParameters, std::vector<realtype> parameters)¶ Constructor.
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SimulationParameters
(std::vector<realtype> fixedParameters, std::vector<realtype> parameters, std::vector<int> plist)¶ Constructor.
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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. Overrides Solver::newton_preeq
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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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