Class CVodeSolver

Inheritance Relationships

Base Type

Class Documentation

class amici::CVodeSolver : public amici::Solver

The CVodeSolver class is a wrapper around the SUNDIALS CVODES solver.

Public Functions

~CVodeSolver() override = default
virtual Solver *clone() const override

Clone this instance.

Returns

The clone

virtual void reInit(realtype t0, const AmiVector &yy0, const AmiVector &yp0) const override

Reinitializes the states in the solver after an event occurrence.

Parameters

  • t0 – reinitialization timepoint

  • yy0 – initial state variables

  • yp0 – initial derivative state variables (DAE only)

virtual void sensReInit(const AmiVectorArray &yyS0, const AmiVectorArray &ypS0) const override

Reinitializes the state sensitivities in the solver after an event occurrence.

Parameters

  • yyS0 – new state sensitivity

  • ypS0 – new derivative state sensitivities (DAE only)

virtual void sensToggleOff() const override

Switches off computation of state sensitivities without deallocating the memory for sensitivities.

virtual void reInitB(int which, realtype tB0, const AmiVector &yyB0, const AmiVector &ypB0) const override

Reinitializes the adjoint states after an event occurrence.

Parameters

  • which – identifier of the backwards problem

  • tB0 – reinitialization timepoint

  • yyB0 – new adjoint state

  • ypB0 – new adjoint derivative state

virtual void quadReInitB(int which, const AmiVector &yQB0) const override

Reinitialize the adjoint states after an event occurrence.

Parameters

  • which – identifier of the backwards problem

  • yQB0 – new adjoint quadrature state

virtual int solve(realtype tout, int itask) const override

Solves the forward problem until a predefined timepoint.

Parameters

  • tout – timepoint until which simulation should be performed

  • itask – task identifier, can be CV_NORMAL or CV_ONE_STEP

Returns

status flag indicating success of execution

virtual int solveF(realtype tout, int itask, int *ncheckPtr) const override

Solves the forward problem until a predefined timepoint (adjoint only)

Parameters

  • tout – timepoint until which simulation should be performed

  • itask – task identifier, can be CV_NORMAL or CV_ONE_STEP

  • ncheckPtr – pointer to a number that counts the internal checkpoints

Returns

status flag indicating success of execution

virtual void solveB(realtype tBout, int itaskB) const override

Solves the backward problem until a predefined timepoint (adjoint only)

Parameters

  • tBout – timepoint until which simulation should be performed

  • itaskB – task identifier, can be CV_NORMAL or CV_ONE_STEP

virtual void getDky(realtype t, int k) const override

interpolates the (derivative of the) solution at the requested timepoint

Parameters

  • t – timepoint

  • k – derivative order

virtual void getSensDky(realtype t, int k) const override

interpolates the (derivative of the) solution at the requested timepoint

Parameters

  • t – timepoint

  • k – derivative order

virtual void getQuadDkyB(realtype t, int k, int which) const override

interpolates the (derivative of the) solution at the requested timepoint

Parameters

  • t – timepoint

  • k – derivative order

  • which – index of backward problem

virtual void getDkyB(realtype t, int k, int which) const override

interpolates the (derivative of the) solution at the requested timepoint

Parameters

  • t – timepoint

  • k – derivative order

  • which – index of backward problem

virtual void getRootInfo(int *rootsfound) const override

getRootInfo extracts information which event occurred

Parameters

rootsfound – array with flags indicating whether the respective event occurred

virtual void setStopTime(realtype tstop) const override

Sets a timepoint at which the simulation will be stopped.

Parameters

tstop – timepoint until which simulation should be performed

virtual void turnOffRootFinding() const override

Disable rootfinding.

virtual const Model *getModel() const override

Accessor function to the model stored in the user data

Returns

user data model

virtual void setLinearSolver() const override

Sets the linear solver for the forward problem.

virtual void setLinearSolverB(int which) const override

Sets the linear solver for the backward problem.

Parameters

which – index of the backward problem

virtual void setNonLinearSolver() const override

Set the non-linear solver for the forward problem.

virtual void setNonLinearSolverSens() const override

Set the non-linear solver for sensitivities.

virtual void setNonLinearSolverB(int which) const override

Set the non-linear solver for the backward problem.

Parameters

which – index of the backward problem

Solver() = default

Default constructor.

Solver(AmiciApplication *app)

Constructor.

Parameters

app – AMICI application context

Solver(const Solver &other)

Solver copy constructor.

Parameters

other –

Protected Functions

virtual void calcIC(realtype tout1) const override

Calculates consistent initial conditions, assumes initial states to be correct (DAE only)

Parameters

tout1 – next timepoint to be computed (sets timescale)

virtual void calcICB(int which, realtype tout1) const override

Calculates consistent initial conditions for the backwards problem, assumes initial states to be correct (DAE only)

Parameters

  • which – identifier of the backwards problem

  • tout1 – next timepoint to be computed (sets timescale)

virtual void getB(int which) const override

extracts the adjoint state at the current timepoint from solver memory and writes it to the xB member variable

Parameters

which – index of the backwards problem

virtual void getSens() const override

extracts the state sensitivity at the current timepoint from solver memory and writes it to the sx member variable

virtual void getQuadB(int which) const override

extracts the adjoint quadrature state at the current timepoint from solver memory and writes it to the xQB member variable

Parameters

which – index of the backwards problem

virtual void getQuad(realtype &t) const override

extracts the quadrature at the current timepoint from solver memory and writes it to the xQ member variable

Parameters

t – timepoint for quadrature extraction

virtual void getQuadDky(realtype t, int k) const override

interpolates the (derivative of the) solution at the requested timepoint

Parameters

  • t – timepoint

  • k – derivative order

virtual void reInitPostProcessF(realtype tnext) const override

reInitPostProcessF postprocessing of the solver memory after a discontinuity in the forward problem

Parameters

tnext – next timepoint (defines integration direction)

virtual void reInitPostProcessB(realtype tnext) const override

reInitPostProcessB postprocessing of the solver memory after a discontinuity in the backward problem

Parameters

tnext – next timepoint (defines integration direction)

void reInitPostProcess(void *cv_mem, realtype *t, AmiVector *yout, realtype tout) const

Postprocessing of the solver memory after a discontinuity.

Parameters

  • cv_mem – pointer to CVODES solver memory object

  • t – pointer to integration time

  • yout – new state vector

  • tout – anticipated next integration timepoint.

virtual void allocateSolver() const override

Create specifies solver method and initializes solver memory for the forward problem.

virtual void setSStolerances(double rtol, double atol) const override

sets scalar relative and absolute tolerances for the forward problem

Parameters

  • rtol – relative tolerances

  • atol – absolute tolerances

virtual void setSensSStolerances(double rtol, const double *atol) const override

activates sets scalar relative and absolute tolerances for the sensitivity variables

Parameters

  • rtol – relative tolerances

  • atol – array of absolute tolerances for every sensitivity variable

virtual void setSensErrCon(bool error_corr) const override

SetSensErrCon specifies whether error control is also enforced for sensitivities for the forward problem

Parameters

error_corr – activation flag

virtual void setQuadErrConB(int which, bool flag) const override

Specifies whether error control is also enforced for the backward quadrature problem.

Parameters

  • which – identifier of the backwards problem

  • flag – activation flag

virtual void setQuadErrCon(bool flag) const override

Specifies whether error control is also enforced for the forward quadrature problem.

Parameters

flag – activation flag

virtual void setErrHandlerFn() const override

Attaches the error handler function (errMsgIdAndTxt) to the solver.

virtual void setUserData() const override

Attaches the user data to the forward problem.

virtual void setUserDataB(int which) const override

attaches the user data to the backward problem

Parameters

which – identifier of the backwards problem

virtual void setMaxNumSteps(long int mxsteps) const override

specifies the maximum number of steps for the forward problem

Note

in contrast to the SUNDIALS method, this sets the overall maximum, not the maximum between output times.

Parameters

mxsteps – number of steps

virtual void setStabLimDet(int stldet) const override

activates stability limit detection for the forward problem

Parameters

stldet – flag for stability limit detection (TRUE or FALSE)

virtual void setStabLimDetB(int which, int stldet) const override

activates stability limit detection for the backward problem

Parameters

  • which – identifier of the backwards problem

  • stldet – flag for stability limit detection (TRUE or FALSE)

virtual void setId(const Model *model) const override

specify algebraic/differential components (DAE only)

Parameters

model – model specification

virtual void setSuppressAlg(bool flag) const override

deactivates error control for algebraic components (DAE only)

Parameters

flag – deactivation flag

void resetState(void *cv_mem, const_N_Vector y0) const

resetState reset the CVODES solver to restart integration after a rhs discontinuity.

Parameters

  • cv_mem – pointer to CVODES solver memory object

  • y0 – new state vector

virtual void setSensParams(const realtype *p, const realtype *pbar, const int *plist) const override

specifies the scaling and indexes for sensitivity computation

Parameters

  • p – parameters

  • pbar – parameter scaling constants

  • plist – parameter index list

virtual void adjInit() const override

initializes the adjoint problem

virtual void quadInit(const AmiVector &xQ0) const override

initializes the quadratures

Parameters

xQ0 – vector with initial values for xQ

virtual void allocateSolverB(int *which) const override

Specifies solver method and initializes solver memory for the backward problem.

Parameters

which – identifier of the backwards problem

virtual void setSStolerancesB(int which, realtype relTolB, realtype absTolB) const override

sets relative and absolute tolerances for the backward problem

Parameters

  • which – identifier of the backwards problem

  • relTolB – relative tolerances

  • absTolB – absolute tolerances

virtual void quadSStolerancesB(int which, realtype reltolQB, realtype abstolQB) const override

sets relative and absolute tolerances for the quadrature backward problem

Parameters

  • which – identifier of the backwards problem

  • reltolQB – relative tolerances

  • abstolQB – absolute tolerances

virtual void quadSStolerances(realtype reltolQ, realtype abstolQ) const override

sets relative and absolute tolerances for the quadrature problem

Parameters

  • reltolQB – relative tolerances

  • abstolQB – absolute tolerances

virtual void setMaxNumStepsB(int which, long int mxstepsB) const override

specifies the maximum number of steps for the forward problem

Note

in contrast to the SUNDIALS method, this sets the overall maximum, not the maximum between output times.

Parameters

  • which – identifier of the backwards problem

  • mxstepsB – number of steps

virtual void diag() const override

attaches a diagonal linear solver to the forward problem

virtual void diagB(int which) const override

attaches a diagonal linear solver to the backward problem

Parameters

which – identifier of the backwards problem

virtual void getNumSteps(const void *ami_mem, long int *numsteps) const override

reports the number of solver steps

Parameters

  • ami_mem – pointer to the solver memory instance (can be from forward or backward problem)

  • numsteps – output array

virtual void getNumRhsEvals(const void *ami_mem, long int *numrhsevals) const override

reports the number of right hand evaluations

Parameters

  • ami_mem – pointer to the solver memory instance (can be from forward or backward problem)

  • numrhsevals – output array

virtual void getNumErrTestFails(const void *ami_mem, long int *numerrtestfails) const override

reports the number of local error test failures

Parameters

  • ami_mem – pointer to the solver memory instance (can be from forward or backward problem)

  • numerrtestfails – output array

virtual void getNumNonlinSolvConvFails(const void *ami_mem, long int *numnonlinsolvconvfails) const override

reports the number of nonlinear convergence failures

Parameters

  • ami_mem – pointer to the solver memory instance (can be from forward or backward problem)

  • numnonlinsolvconvfails – output array

virtual void getLastOrder(const void *ami_ami_mem, int *order) const override

Reports the order of the integration method during the last internal step.

Parameters

  • ami_mem – pointer to the solver memory instance (can be from forward or backward problem)

  • order – output array

virtual void *getAdjBmem(void *ami_mem, int which) const override

Retrieves the solver memory instance for the backward problem.

Parameters

  • which – identifier of the backwards problem

  • ami_mem – pointer to the forward solver memory instance

Returns

A (void *) pointer to the CVODES memory allocated for the backward problem.

virtual void init(realtype t0, const AmiVector &x0, const AmiVector &dx0) const override

Initializes the states at the specified initial timepoint.

Parameters

  • t0 – initial timepoint

  • x0 – initial states

  • dx0 – initial derivative states

virtual void initSteadystate(const realtype t0, const AmiVector &x0, const AmiVector &dx0) const override

Initializes the states at the specified initial timepoint.

Parameters

  • t0 – initial timepoint

  • x0 – initial states

  • dx0 – initial derivative states

virtual void sensInit1(const AmiVectorArray &sx0, const AmiVectorArray &sdx0) const override

Initializes the forward sensitivities.

Parameters

  • sx0 – initial states sensitivities

  • sdx0 – initial derivative states sensitivities

virtual void binit(int which, realtype tf, const AmiVector &xB0, const AmiVector &dxB0) const override

Initialize the adjoint states at the specified final timepoint.

Parameters

  • which – identifier of the backwards problem

  • tf – final timepoint

  • xB0 – initial adjoint state

  • dxB0 – initial adjoint derivative state

virtual void qbinit(int which, const AmiVector &xQB0) const override

Initialize the quadrature states at the specified final timepoint.

Parameters

  • which – identifier of the backwards problem

  • xQB0 – initial adjoint quadrature state

virtual void rootInit(int ne) const override

Initializes the rootfinding for events.

Parameters

ne – number of different events

virtual void setDenseJacFn() const override

Set the dense Jacobian function.

virtual void setSparseJacFn() const override

sets the sparse Jacobian function

virtual void setBandJacFn() const override

sets the banded Jacobian function

virtual void setJacTimesVecFn() const override

sets the Jacobian vector multiplication function

virtual void setDenseJacFnB(int which) const override

sets the dense Jacobian function

Parameters

which – identifier of the backwards problem

virtual void setSparseJacFnB(int which) const override

sets the sparse Jacobian function

Parameters

which – identifier of the backwards problem

virtual void setBandJacFnB(int which) const override

sets the banded Jacobian function

Parameters

which – identifier of the backwards problem

virtual void setJacTimesVecFnB(int which) const override

sets the Jacobian vector multiplication function

Parameters

which – identifier of the backwards problem

virtual void setSparseJacFn_ss() const override

sets the sparse Jacobian function for backward steady state case

Friends

template<class Archive>
friend void serialize(Archive &ar, CVodeSolver &s, unsigned int)

Serialize amici::CVodeSolver to boost archive.

Parameters

  • ar – Archive

  • s – Solver instance to serialize

friend bool operator==(const CVodeSolver &a, const CVodeSolver &b)

Equality operator.

Parameters

  • a –

  • b –

Returns

Whether a and b are equal