Class SteadystateProblem

Class Documentation

class amici::SteadystateProblem

The SteadystateProblem class solves a steady-state problem using Newton’s method and falls back to integration on failure.

Public Functions

explicit SteadystateProblem(const Solver &solver, const Model &model)

constructor

Parameters
void workSteadyStateProblem(const Solver &solver, Model &model, int it)

Handles steady state computation in the forward case: tries to determine the steady state of the ODE system and computes steady state sensitivities if requested.

Parameters

  • solver – pointer to the solver object

  • model – pointer to the model object

  • it – integer with the index of the current time step

void workSteadyStateBackwardProblem(const Solver &solver, Model &model, const BackwardProblem *bwd)

Integrates over the adjoint state backward in time by solving a linear system of equations, which gives the analytical solution. Computes the gradient via adjoint steady state sensitivities

Parameters

  • solver – pointer to the solver object

  • model – pointer to the model object

  • bwd – backward problem

inline const SimulationState &getFinalSimulationState() const

Returns the stored SimulationState.

Returns

stored SimulationState

inline const AmiVector &getEquilibrationQuadratures() const

Returns the quadratures from pre- or postequilibration.

Returns

xQB Vector with quadratures

inline const AmiVector &getState() const

Returns state at steadystate.

Returns

x

inline const AmiVectorArray &getStateSensitivity() const

Returns state sensitivity at steadystate.

Returns

sx

inline std::vector<realtype> const &getDJydx() const

Accessor for dJydx.

Returns

dJydx

inline double getCPUTime() const

Accessor for run_time of the forward problem.

Returns

run_time

inline double getCPUTimeB() const

Accessor for run_time of the backward problem.

Returns

run_time

inline std::vector<SteadyStateStatus> const &getSteadyStateStatus() const

Accessor for steady_state_status.

Returns

steady_state_status

inline realtype getSteadyStateTime() const

Get model time at which steadystate was found through simulation.

Returns

t

inline realtype getResidualNorm() const

Accessor for wrms.

Returns

wrms

inline const std::vector<int> &getNumSteps() const

Accessor for numsteps.

Returns

numsteps

inline int getNumStepsB() const

Accessor for numstepsB.

Returns

numstepsB

void getAdjointUpdates(Model &model, const ExpData &edata)

computes adjoint updates dJydx according to provided model and expdata

Parameters

  • model – Model instance

  • edata – experimental data

inline AmiVector const &getAdjointState() const

Return the adjoint state.

Returns

xB adjoint state

inline AmiVector const &getAdjointQuadrature() const

Accessor for xQB.

Returns

xQB

inline bool hasQuadrature() const

Accessor for hasQuadrature_.

Returns

hasQuadrature_

bool checkSteadyStateSuccess() const

computes adjoint updates dJydx according to provided model and expdata

Returns

convergence of steady state solver