Class CVodeSolver

Inheritance Relationships

Base Type

Class Documentation

class 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

inline virtual std::string get_class_name() const override

Get the name of this class.

Returns:

Class name.

virtual void reinit(realtype t0, AmiVector const &yy0, AmiVector const &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 sens_reinit(AmiVectorArray const &yyS0, AmiVectorArray const &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 sens_toggle_off() const override

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

virtual void reinit_b(int which, realtype tB0, AmiVector const &yyB0, AmiVector const &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 reinit_quad_b(int which, AmiVector const &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 solve_f(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 solve_b(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 get_dky(realtype t, int k) const override

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

Parameters:

  • t – timepoint

  • k – derivative order

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

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

Parameters:

  • t – timepoint

  • k – derivative order

virtual void get_quad_dky_b(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 get_dky_b(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 get_root_info(int *rootsfound) const override

get_root_info extracts information which event occurred

Parameters:

rootsfound – array with flags indicating whether the respective event occurred

virtual void set_stop_time(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 turn_off_root_finding() const override

Disable rootfinding.

virtual Model const *get_model() const override

Accessor function to the model stored in the user data

Returns:

user data model

virtual void set_linear_solver() const override

Sets the linear solver for the forward problem.

virtual void set_linear_solver_b(int which) const override

Sets the linear solver for the backward problem.

Parameters:

which – index of the backward problem

virtual void set_non_linear_solver() const override

Set the non-linear solver for the forward problem.

virtual void set_non_linear_solver_sens() const override

Set the non-linear solver for sensitivities.

virtual void set_non_linear_solver_b(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(Solver const &other)

Solver copy constructor.

Parameters:

other –

Protected Functions

virtual void calc_ic(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 calc_ic_b(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 get_b(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 get_sens() const override

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

virtual void get_quad_b(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 get_quad(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 get_quad_dky(realtype t, int k) const override

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

Parameters:

  • t – timepoint

  • k – derivative order

virtual void reinit_post_process_f(realtype tnext) const override

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

Parameters:

tnext – next timepoint (defines integration direction)

virtual void reinit_post_process_b(realtype tnext) const override

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

Parameters:

tnext – next timepoint (defines integration direction)

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

Post-processing 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 allocate_solver() const override

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

virtual void set_ss_tolerances(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 set_sens_ss_tolerances(double rtol, double const *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 set_sens_err_con(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 set_quad_err_con_b(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 set_quad_err_con(bool flag) const override

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

Parameters:

flag – activation flag

virtual void set_user_data() const override

Attaches the user data to the forward problem.

virtual void set_user_data_b(int which) const override

attaches the user data to the backward problem

Parameters:

which – identifier of the backwards problem

virtual void set_max_num_steps(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 set_stab_lim_det(int stldet) const override

activates stability limit detection for the forward problem

Parameters:

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

virtual void set_stab_lim_det_b(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 set_id(Model const *model) const override

specify algebraic/differential components (DAE only)

Parameters:

model – model specification

virtual void set_suppress_alg(bool flag) const override

deactivates error control for algebraic components (DAE only)

Parameters:

flag – deactivation flag

void reset_state(void *cv_mem, const_N_Vector y0) const

reset_state 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 set_sens_params(realtype const *p, realtype const *pbar, int const *plist) const override

specifies the scaling and indexes for sensitivity computation

Parameters:

  • p – parameters

  • pbar – parameter scaling constants

  • plist – parameter index list

virtual void adj_init() const override

initializes the adjoint problem

virtual void quad_init(AmiVector const &xQ0) const override

initializes the quadratures

Parameters:

xQ0 – vector with initial values for xQ

virtual void allocate_solver_b(int *which) const override

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

Parameters:

which – identifier of the backwards problem

virtual void set_ss_tolerances_b(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 quad_ss_tolerances_b(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 quad_ss_tolerances(realtype reltolQ, realtype abstolQ) const override

sets relative and absolute tolerances for the quadrature problem

Parameters:

  • reltolQB – relative tolerances

  • abstolQB – absolute tolerances

virtual void set_max_num_steps_b(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 diag_b(int which) const override

attaches a diagonal linear solver to the backward problem

Parameters:

which – identifier of the backwards problem

virtual void get_num_steps(void const *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 get_num_rhs_evals(void const *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 get_num_err_test_fails(void const *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 get_num_non_lin_solv_conv_fails(void const *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 get_last_order(void const *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 *get_adj_b_mem(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, AmiVector const &x0, AmiVector const &dx0) const override

Initializes the states at the specified initial timepoint.

Parameters:

  • t0 – initial timepoint

  • x0 – initial states

  • dx0 – initial derivative states

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

Initializes the states at the specified initial timepoint.

Parameters:

  • t0 – initial timepoint

  • x0 – initial states

  • dx0 – initial derivative states

virtual void sens_init_1(AmiVectorArray const &sx0, AmiVectorArray const &sdx0) const override

Initializes the forward sensitivities.

Parameters:

  • sx0 – initial states sensitivities

  • sdx0 – initial derivative states sensitivities

virtual void b_init(int which, realtype tf, AmiVector const &xB0, AmiVector const &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 qb_init(int which, AmiVector const &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 root_init(int ne) const override

Initializes the root-finding for events.

Parameters:

ne – number of different events

virtual void set_dense_jac_fn() const override

Set the dense Jacobian function.

virtual void set_sparse_jac_fn() const override

sets the sparse Jacobian function

virtual void set_band_jac_fn() const override

sets the banded Jacobian function

virtual void set_jac_times_vec_fn() const override

sets the Jacobian vector multiplication function

virtual void set_dense_jac_fn_b(int which) const override

sets the dense Jacobian function

Parameters:

which – identifier of the backwards problem

virtual void set_sparse_jac_fn_b(int which) const override

sets the sparse Jacobian function

Parameters:

which – identifier of the backwards problem

virtual void set_band_jac_fn_b(int which) const override

sets the banded Jacobian function

Parameters:

which – identifier of the backwards problem

virtual void set_jac_times_vec_fn_b(int which) const override

sets the Jacobian vector multiplication function

Parameters:

which – identifier of the backwards problem

virtual void set_sparse_jac_fn_ss() const override

sets the sparse Jacobian function for backward steady state case

virtual void apply_max_nonlin_iters() const override

Apply the maximum number of nonlinear solver iterations permitted per step.

virtual void apply_max_conv_fails() const override

Apply the maximum number of nonlinear solver convergence failures permitted per step.

virtual void apply_constraints() const override

Apply the constraints to the solver.

virtual void apply_max_step_size() const override

Apply the allowed maximum stepsize to the solver.

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==(CVodeSolver const &a, CVodeSolver const &b)

Equality operator.

Parameters:

  • a –

  • b –

Returns:

Whether a and b are equal