Class ForwardProblem

Class Documentation

class amici::ForwardProblem

The ForwardProblem class groups all functions for solving the forward problem.

Public Functions

ForwardProblem(const ExpData *edata, Model *model, Solver *solver, const SteadystateProblem *preeq)

Constructor.

Parameters

  • edata – pointer to ExpData instance

  • model – pointer to Model instance

  • solver – pointer to Solver instance

  • preeq – preequilibration with which to initialize the forward problem, pass nullptr for no initialization

~ForwardProblem() = default
void workForwardProblem()

Solve the forward problem.

If forward sensitivities are enabled this will also compute sensitivities.

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 realtype getTime() const

Accessor for t.

Returns

t

inline AmiVector const &getState() const

Accessor for x.

Returns

x

inline AmiVector const &getStateDerivative() const

Accessor for dx.

Returns

dx

inline AmiVectorArray const &getStateSensitivity() const

Accessor for sx.

Returns

sx

inline std::vector<AmiVector> const &getStatesAtDiscontinuities() const

Accessor for x_disc.

Returns

x_disc

inline std::vector<AmiVector> const &getRHSAtDiscontinuities() const

Accessor for xdot_disc.

Returns

xdot_disc

inline std::vector<AmiVector> const &getRHSBeforeDiscontinuities() const

Accessor for xdot_old_disc.

Returns

xdot_old_disc

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

Accessor for nroots.

Returns

nroots

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

Accessor for discs.

Returns

discs

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

Accessor for rootidx.

Returns

rootidx

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

Accessor for dJydx.

Returns

dJydx

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

Accessor for dJzdx.

Returns

dJzdx

inline AmiVector *getStatePointer()

Accessor for pointer to x.

Returns

&x

inline AmiVector *getStateDerivativePointer()

Accessor for pointer to dx.

Returns

&dx

inline AmiVectorArray *getStateSensitivityPointer()

accessor for pointer to sx

Returns

&sx

inline AmiVectorArray *getStateDerivativeSensitivityPointer()

Accessor for pointer to sdx.

Returns

&sdx

inline int getCurrentTimeIteration() const

Accessor for it.

Returns

it

inline realtype getFinalTime() const

Returns final time point for which simulations are available.

Returns

time point

inline int getEventCounter() const

Returns maximal event index for which simulations are available.

Returns

index

inline int getRootCounter() const

Returns maximal event index for which the timepoint is available.

Returns

index

inline const SimulationState &getSimulationStateTimepoint(int it) const

Retrieves the carbon copy of the simulation state variables at the specified timepoint index.

Parameters

it – timepoint index

Returns

state

inline const SimulationState &getSimulationStateEvent(int iroot) const

Retrieves the carbon copy of the simulation state variables at the specified event index.

Parameters

iroot – event index

Returns

SimulationState

inline const SimulationState &getInitialSimulationState() const

Retrieves the carbon copy of the simulation state variables at the initial timepoint.

Returns

SimulationState

inline const SimulationState &getFinalSimulationState() const

Retrieves the carbon copy of the simulation state variables at the final timepoint (or when simulation failed)

Returns

SimulationState

Public Members

Model *model

pointer to model instance

Solver *solver

pointer to solver instance

const ExpData *edata

pointer to experimental data instance