Class Model_ODE

Inheritance Relationships

Base Type

Class Documentation

class amici::Model_ODE : public amici::Model

The Model class represents an AMICI ODE model.

The model does not contain any data, but represents the state of the model at a specific time t. The states must not always be in sync, but may be updated asynchronously.

Public Functions

Model_ODE() = default

default constructor

Model_ODE(ModelDimensions const &model_dimensions, SimulationParameters simulation_parameters, const SecondOrderMode o2mode, std::vector<realtype> const &idlist, std::vector<int> const &z2event, const bool pythonGenerated = false, const int ndxdotdp_explicit = 0, const int ndxdotdx_explicit = 0, const int w_recursion_depth = 0)

Constructor with model dimensions.

Parameters

  • model_dimensions: Model dimensions

  • simulation_parameters: Simulation parameters

  • o2mode: second order sensitivity mode

  • idlist: indexes indicating algebraic components (DAE only)

  • z2event: mapping of event outputs to events

  • pythonGenerated: flag indicating matlab or python wrapping

  • ndxdotdp_explicit: number of nonzero elements dxdotdp_explicit

  • ndxdotdx_explicit: number of nonzero elements dxdotdx_explicit

  • w_recursion_depth: Recursion depth of fw

void fJ(realtype t, realtype cj, const AmiVector &x, const AmiVector &dx, const AmiVector &xdot, SUNMatrix J) override

Dense Jacobian function.

Parameters

  • t: time

  • cj: scaling factor (inverse of timestep, DAE only)

  • x: state

  • dx: time derivative of state (DAE only)

  • xdot: values of residual function (unused)

  • J: dense matrix to which values of the jacobian will be written

void fJ(realtype t, const_N_Vector x, const_N_Vector xdot, SUNMatrix J)

Implementation of fJ at the N_Vector level.

This function provides an interface to the model specific routines for the solver implementation as well as the AmiVector level implementation

Parameters

  • t: timepoint

  • x: Vector with the states

  • xdot: Vector with the right hand side

  • J: Matrix to which the Jacobian will be written

void fJB(const realtype t, realtype cj, const AmiVector &x, const AmiVector &dx, const AmiVector &xB, const AmiVector &dxB, const AmiVector &xBdot, SUNMatrix JB) override

Dense Jacobian function.

Parameters

  • t: time

  • cj: scaling factor (inverse of timestep, DAE only)

  • x: state

  • dx: time derivative of state (DAE only)

  • xB: Vector with the adjoint states

  • dxB: Vector with the adjoint derivative states

  • xBdot: Vector with the adjoint right hand side (unused)

  • JB: dense matrix to which values of the jacobian will be written

void fJB(realtype t, const_N_Vector x, const_N_Vector xB, const_N_Vector xBdot, SUNMatrix JB)

Implementation of fJB at the N_Vector level, this function provides an interface to the model specific routines for the solver implementation.

Parameters

  • t: timepoint

  • x: Vector with the states

  • xB: Vector with the adjoint states

  • xBdot: Vector with the adjoint right hand side

  • JB: Matrix to which the Jacobian will be written

void fJSparse(realtype t, realtype cj, const AmiVector &x, const AmiVector &dx, const AmiVector &xdot, SUNMatrix J) override

Sparse Jacobian function.

Parameters

  • t: time

  • cj: scaling factor (inverse of timestep, DAE only)

  • x: state

  • dx: time derivative of state (DAE only)

  • xdot: values of residual function (unused)

  • J: sparse matrix to which values of the Jacobian will be written

void fJSparse(realtype t, const_N_Vector x, SUNMatrix J)

Implementation of fJSparse at the N_Vector level, this function provides an interface to the model specific routines for the solver implementation as well as the AmiVector level implementation.

Parameters

  • t: timepoint

  • x: Vector with the states

  • J: Matrix to which the Jacobian will be written

void fJSparseB(const realtype t, realtype cj, const AmiVector &x, const AmiVector &dx, const AmiVector &xB, const AmiVector &dxB, const AmiVector &xBdot, SUNMatrix JB) override

Sparse Jacobian function.

Parameters

  • t: time

  • cj: scaling factor (inverse of timestep, DAE only)

  • x: state

  • dx: time derivative of state (DAE only)

  • xB: Vector with the adjoint states

  • dxB: Vector with the adjoint derivative states

  • xBdot: Vector with the adjoint right hand side (unused)

  • JB: dense matrix to which values of the jacobian will be written

void fJSparseB(realtype t, const_N_Vector x, const_N_Vector xB, const_N_Vector xBdot, SUNMatrix JB)

Implementation of fJSparseB at the N_Vector level, this function provides an interface to the model specific routines for the solver implementation.

Parameters

  • t: timepoint

  • x: Vector with the states

  • xB: Vector with the adjoint states

  • xBdot: Vector with the adjoint right hand side

  • JB: Matrix to which the Jacobian will be written

void fJDiag(realtype t, N_Vector JDiag, const_N_Vector x)

Implementation of fJDiag at the N_Vector level, this function provides an interface to the model specific routines for the solver implementation.

Parameters

  • t: timepoint

  • JDiag: Vector to which the Jacobian diagonal will be written

  • x: Vector with the states

void fJDiag(realtype t, AmiVector &JDiag, realtype cj, const AmiVector &x, const AmiVector &dx) override

Diagonal of the Jacobian (for preconditioning)

Parameters

  • t: timepoint

  • JDiag: Vector to which the Jacobian diagonal will be written

  • cj: scaling factor, inverse of the step size

  • x: Vector with the states

  • dx: Vector with the derivative states

void fJv(realtype t, const AmiVector &x, const AmiVector &dx, const AmiVector &xdot, const AmiVector &v, AmiVector &nJv, realtype cj) override

Jacobian multiply function.

Parameters

  • t: time

  • x: state

  • dx: time derivative of state (DAE only)

  • xdot: values of residual function (unused)

  • v: multiplication vector (unused)

  • nJv: array to which result of multiplication will be written

  • cj: scaling factor (inverse of timestep, DAE only)

void fJv(const_N_Vector v, N_Vector Jv, realtype t, const_N_Vector x)

Implementation of fJv at the N_Vector level.

Parameters

  • t: timepoint

  • x: Vector with the states

  • v: Vector with which the Jacobian is multiplied

  • Jv: Vector to which the Jacobian vector product will be written

void fJvB(const_N_Vector vB, N_Vector JvB, realtype t, const_N_Vector x, const_N_Vector xB)

Implementation of fJvB at the N_Vector level.

Parameters

  • t: timepoint

  • x: Vector with the states

  • xB: Vector with the adjoint states

  • vB: Vector with which the Jacobian is multiplied

  • JvB: Vector to which the Jacobian vector product will be written

void froot(realtype t, const AmiVector &x, const AmiVector &dx, gsl::span<realtype> root) override

Root function.

Parameters

  • t: time

  • x: state

  • dx: time derivative of state (DAE only)

  • root: array to which values of the root function will be written

void froot(realtype t, const_N_Vector x, gsl::span<realtype> root)

Implementation of froot at the N_Vector level This function provides an interface to the model specific routines for the solver implementation as well as the AmiVector level implementation.

Parameters

  • t: timepoint

  • x: Vector with the states

  • root: array with root function values

void fxdot(realtype t, const AmiVector &x, const AmiVector &dx, AmiVector &xdot) override

Residual function.

Parameters

  • t: time

  • x: state

  • dx: time derivative of state (DAE only)

  • xdot: array to which values of the residual function will be written

void fxdot(realtype t, const_N_Vector x, N_Vector xdot)

Implementation of fxdot at the N_Vector level, this function provides an interface to the model specific routines for the solver implementation as well as the AmiVector level implementation.

Parameters

  • t: timepoint

  • x: Vector with the states

  • xdot: Vector with the right hand side

void fxBdot(realtype t, N_Vector x, N_Vector xB, N_Vector xBdot)

Implementation of fxBdot at the N_Vector level.

Parameters

  • t: timepoint

  • x: Vector with the states

  • xB: Vector with the adjoint states

  • xBdot: Vector with the adjoint right hand side

void fqBdot(realtype t, const_N_Vector x, const_N_Vector xB, N_Vector qBdot)

Implementation of fqBdot at the N_Vector level.

Parameters

  • t: timepoint

  • x: Vector with the states

  • xB: Vector with the adjoint states

  • qBdot: Vector with the adjoint quadrature right hand side

void fxBdot_ss(const realtype t, const AmiVector &xB, const AmiVector&, AmiVector &xBdot) override

Residual function backward when running in steady state mode.

Parameters

  • t: time

  • xB: adjoint state

  • dxB: time derivative of state (DAE only)

  • xBdot: array to which values of the residual function will be written

void fxBdot_ss(realtype t, const_N_Vector xB, N_Vector xBdot) const

Implementation of fxBdot for steady state at the N_Vector level.

Parameters

  • t: timepoint

  • xB: Vector with the states

  • xBdot: Vector with the adjoint right hand side

void fqBdot_ss(realtype t, N_Vector xB, N_Vector qBdot) const

Implementation of fqBdot for steady state case at the N_Vector level.

Parameters

  • t: timepoint

  • xB: Vector with the adjoint states

  • qBdot: Vector with the adjoint quadrature right hand side

void fJSparseB_ss(SUNMatrix JB) override

Sparse Jacobian function backward, steady state case.

Parameters

  • JB: sparse matrix to which values of the Jacobian will be written

void writeSteadystateJB(const realtype t, realtype cj, const AmiVector &x, const AmiVector &dx, const AmiVector &xB, const AmiVector &dxB, const AmiVector &xBdot) override

Computes the sparse backward Jacobian for steadystate integration and writes it to the model member.

Parameters

  • t: timepoint

  • cj: scalar in Jacobian

  • x: Vector with the states

  • dx: Vector with the derivative states

  • xB: Vector with the adjoint states

  • dxB: Vector with the adjoint derivative states

  • xBdot: Vector with the adjoint state right hand side

void fsxdot(realtype t, const AmiVector &x, const AmiVector &dx, int ip, const AmiVector &sx, const AmiVector &sdx, AmiVector &sxdot) override

Sensitivity Residual function.

Parameters

  • t: time

  • x: state

  • dx: time derivative of state (DAE only)

  • ip: parameter index

  • sx: sensitivity state

  • sdx: time derivative of sensitivity state (DAE only)

  • sxdot: array to which values of the sensitivity residual function will be written

void fsxdot(realtype t, const_N_Vector x, int ip, const_N_Vector sx, N_Vector sxdot)

Implementation of fsxdot at the N_Vector level.

Parameters

  • t: timepoint

  • x: Vector with the states

  • ip: parameter index

  • sx: Vector with the state sensitivities

  • sxdot: Vector with the sensitivity right hand side

std::unique_ptr<Solver> getSolver() override

Retrieves the solver object.

Return

The Solver instance

Protected Functions

void fJSparse(SUNMatrixContent_Sparse JSparse, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx)

Model specific implementation for fJSparse (Matlab)

Parameters

  • JSparse: Matrix to which the Jacobian will be written

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: Heaviside vector

  • w: vector with helper variables

  • dwdx: derivative of w wrt x

void fJSparse(realtype *JSparse, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx)

Model specific implementation for fJSparse, data only (Py)

Parameters

  • JSparse: Matrix to which the Jacobian will be written

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: Heaviside vector

  • w: vector with helper variables

  • dwdx: derivative of w wrt x

void fJSparse_colptrs(SUNMatrixWrapper &JSparse)

Model specific implementation for fJSparse, column pointers.

Parameters

  • JSparse: sparse matrix to which colptrs will be written

void fJSparse_rowvals(SUNMatrixWrapper &JSparse)

Model specific implementation for fJSparse, row values.

Parameters

  • JSparse: sparse matrix to which rowvals will be written

void froot(realtype *root, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h)

Model specific implementation for froot.

Parameters

  • root: values of the trigger function

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: Heaviside vector

void fxdot(realtype *xdot, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w) = 0

Model specific implementation for fxdot.

Parameters

  • xdot: residual function

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: Heaviside vector

  • w: vector with helper variables

void fdxdotdp(realtype *dxdotdp, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, int ip, const realtype *w, const realtype *dwdp)

Model specific implementation of fdxdotdp, with w chainrule (Matlab)

Parameters

  • dxdotdp: partial derivative xdot wrt p

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: Heaviside vector

  • ip: parameter index

  • w: vector with helper variables

  • dwdp: derivative of w wrt p

void fdxdotdp_explicit(realtype *dxdotdp_explicit, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w)

Model specific implementation of fdxdotdp_explicit, no w chainrule (Py)

Parameters

  • dxdotdp_explicit: partial derivative xdot wrt p

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: Heaviside vector

  • w: vector with helper variables

void fdxdotdp_explicit_colptrs(SUNMatrixWrapper &dxdotdp)

Model specific implementation of fdxdotdp_explicit, colptrs part.

Parameters

  • dxdotdp: sparse matrix to which colptrs will be written

void fdxdotdp_explicit_rowvals(SUNMatrixWrapper &dxdotdp)

Model specific implementation of fdxdotdp_explicit, rowvals part.

Parameters

  • dxdotdp: sparse matrix to which rowvals will be written

void fdxdotdx_explicit(realtype *dxdotdx_explicit, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w)

Model specific implementation of fdxdotdx_explicit, no w chainrule (Py)

Parameters

  • dxdotdx_explicit: partial derivative xdot wrt x

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: heavyside vector

  • w: vector with helper variables

void fdxdotdx_explicit_colptrs(SUNMatrixWrapper &dxdotdx)

Model specific implementation of fdxdotdx_explicit, colptrs part.

Parameters

  • dxdotdx: sparse matrix to which colptrs will be written

void fdxdotdx_explicit_rowvals(SUNMatrixWrapper &dxdotdx)

Model specific implementation of fdxdotdx_explicit, rowvals part.

Parameters

  • dxdotdx: sparse matrix to which rowvals will be written

void fdxdotdw(realtype *dxdotdw, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w)

Model specific implementation of fdxdotdw, data part.

Parameters

  • dxdotdw: partial derivative xdot wrt w

  • t: timepoint

  • x: Vector with the states

  • p: parameter vector

  • k: constants vector

  • h: Heaviside vector

  • w: vector with helper variables

void fdxdotdw_colptrs(SUNMatrixWrapper &dxdotdw)

Model specific implementation of fdxdotdw, colptrs part.

Parameters

  • dxdotdw: sparse matrix to which colptrs will be written

void fdxdotdw_rowvals(SUNMatrixWrapper &dxdotdw)

Model specific implementation of fdxdotdw, rowvals part.

Parameters

  • dxdotdw: sparse matrix to which rowvals will be written

void fdxdotdw(realtype t, const_N_Vector x)

Sensitivity of dx/dt wrt model parameters w.

Parameters

  • t: timepoint

  • x: Vector with the states

void fdxdotdp(realtype t, const_N_Vector x)

Explicit sensitivity of dx/dt wrt model parameters p

Parameters

  • t: timepoint

  • x: Vector with the states

void fdxdotdp(realtype t, const AmiVector &x, const AmiVector &dx) override

Model specific sparse implementation of explicit parameter derivative of right hand side.

Parameters

  • t: time

  • x: state

  • dx: time derivative of state (DAE only)