amici.amici.SimulationParameters¶
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class
amici.amici.
SimulationParameters
(*args)[source]¶ Container for various simulation parameters.
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__init__
(*args)[source] Overload 1:
Constructor
- Parameters
timepoints (DoubleVector) – Timepoints for which simulation results are requested
Overload 2:
Constructor
- Parameters
fixedParameters (DoubleVector) – Model constants
parameters (DoubleVector) – Model 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:
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
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__init__
(*args)[source]¶ Overload 1:
Constructor
- Parameters
timepoints (DoubleVector) – Timepoints for which simulation results are requested
Overload 2:
Constructor
- Parameters
fixedParameters (DoubleVector) – Model constants
parameters (DoubleVector) – Model 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
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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
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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
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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
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