Class Model_ODE
Defined in File model_ode.h
Inheritance Relationships
Base Type
public amici::Model
(Class Model)
Class Documentation
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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
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Model_ODE() = default
default constructor
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inline 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
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virtual 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
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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
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virtual 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
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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
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virtual 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
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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
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virtual 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
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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
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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
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virtual 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
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virtual 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)
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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
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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
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virtual 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
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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
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virtual 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
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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
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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
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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
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virtual 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
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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
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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
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virtual 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
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virtual 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
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virtual 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
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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
Protected Functions
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virtual 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
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virtual 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
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virtual void fJSparse_colptrs(SUNMatrixWrapper &JSparse)
Model specific implementation for fJSparse, column pointers.
- Parameters
JSparse – sparse matrix to which colptrs will be written
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virtual void fJSparse_rowvals(SUNMatrixWrapper &JSparse)
Model specific implementation for fJSparse, row values.
- Parameters
JSparse – sparse matrix to which rowvals will be written
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virtual void froot(realtype *root, realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *tcl)
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
tcl – total abundances for conservation laws
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virtual 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
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virtual 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
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virtual 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
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virtual void fdxdotdp_explicit_colptrs(SUNMatrixWrapper &dxdotdp)
Model specific implementation of fdxdotdp_explicit, colptrs part.
- Parameters
dxdotdp – sparse matrix to which colptrs will be written
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virtual void fdxdotdp_explicit_rowvals(SUNMatrixWrapper &dxdotdp)
Model specific implementation of fdxdotdp_explicit, rowvals part.
- Parameters
dxdotdp – sparse matrix to which rowvals will be written
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virtual 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
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virtual void fdxdotdx_explicit_colptrs(SUNMatrixWrapper &dxdotdx)
Model specific implementation of fdxdotdx_explicit, colptrs part.
- Parameters
dxdotdx – sparse matrix to which colptrs will be written
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virtual void fdxdotdx_explicit_rowvals(SUNMatrixWrapper &dxdotdx)
Model specific implementation of fdxdotdx_explicit, rowvals part.
- Parameters
dxdotdx – sparse matrix to which rowvals will be written
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virtual 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
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virtual void fdxdotdw_colptrs(SUNMatrixWrapper &dxdotdw)
Model specific implementation of fdxdotdw, colptrs part.
- Parameters
dxdotdw – sparse matrix to which colptrs will be written
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virtual void fdxdotdw_rowvals(SUNMatrixWrapper &dxdotdw)
Model specific implementation of fdxdotdw, rowvals part.
- Parameters
dxdotdw – sparse matrix to which rowvals will be written
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void fdxdotdw(realtype t, const_N_Vector x)
Sensitivity of dx/dt wrt model parameters w.
- Parameters
t – timepoint
x – Vector with the states
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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
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Model_ODE() = default