Program Listing for File model_ode.h¶
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#ifndef AMICI_MODEL_ODE_H
#define AMICI_MODEL_ODE_H
#include "amici/model.h"
#include <nvector/nvector_serial.h>
#include <sundials/sundials_matrix.h>
#include <sunmatrix/sunmatrix_band.h>
#include <sunmatrix/sunmatrix_dense.h>
#include <sunmatrix/sunmatrix_sparse.h>
#include <utility>
#include <vector>
namespace amici {
class CVodeSolver;
class Model_ODE : public Model {
public:
Model_ODE() = default;
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)
: Model(model_dimensions, simulation_parameters,
o2mode, idlist, z2event, pythonGenerated,
ndxdotdp_explicit, ndxdotdx_explicit, w_recursion_depth) {}
void fJ(realtype t, realtype cj, const AmiVector &x, const AmiVector &dx,
const AmiVector &xdot, SUNMatrix J) override;
void fJ(realtype t, const_N_Vector x, const_N_Vector xdot, SUNMatrix J);
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;
void fJB(realtype t, const_N_Vector x, const_N_Vector xB,
const_N_Vector xBdot, SUNMatrix JB);
void fJSparse(realtype t, realtype cj, const AmiVector &x,
const AmiVector &dx, const AmiVector &xdot,
SUNMatrix J) override;
void fJSparse(realtype t, const_N_Vector x, SUNMatrix J);
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;
void fJSparseB(realtype t, const_N_Vector x, const_N_Vector xB,
const_N_Vector xBdot, SUNMatrix JB);
void fJDiag(realtype t, N_Vector JDiag, const_N_Vector x);
void fJDiag(realtype t, AmiVector &JDiag, realtype cj, const AmiVector &x,
const AmiVector &dx) override;
void fJv(realtype t, const AmiVector &x, const AmiVector &dx,
const AmiVector &xdot, const AmiVector &v, AmiVector &nJv,
realtype cj) override;
void fJv(const_N_Vector v, N_Vector Jv, realtype t, const_N_Vector x);
void fJvB(const_N_Vector vB, N_Vector JvB, realtype t, const_N_Vector x,
const_N_Vector xB);
void froot(realtype t, const AmiVector &x, const AmiVector &dx,
gsl::span<realtype> root) override;
void froot(realtype t, const_N_Vector x, gsl::span<realtype> root);
void fxdot(realtype t, const AmiVector &x, const AmiVector &dx,
AmiVector &xdot) override;
void fxdot(realtype t, const_N_Vector x, N_Vector xdot);
void fxBdot(realtype t, N_Vector x, N_Vector xB, N_Vector xBdot);
void fqBdot(realtype t, const_N_Vector x, const_N_Vector xB, N_Vector qBdot);
void fxBdot_ss(const realtype t, const AmiVector &xB,
const AmiVector & /*dxB*/, AmiVector &xBdot) override;
void fxBdot_ss(realtype t, const_N_Vector xB, N_Vector xBdot) const;
void fqBdot_ss(realtype t, N_Vector xB, N_Vector qBdot) const;
void fJSparseB_ss(SUNMatrix JB) override;
void writeSteadystateJB(const realtype t, realtype cj,
const AmiVector &x, const AmiVector &dx,
const AmiVector &xB, const AmiVector &dxB,
const AmiVector &xBdot) override;
void fsxdot(realtype t, const AmiVector &x, const AmiVector &dx, int ip,
const AmiVector &sx, const AmiVector &sdx,
AmiVector &sxdot) override;
void fsxdot(realtype t, const_N_Vector x, int ip, const_N_Vector sx,
N_Vector sxdot);
std::unique_ptr<Solver> getSolver() override;
protected:
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);
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);
virtual void fJSparse_colptrs(SUNMatrixWrapper &JSparse);
virtual void fJSparse_rowvals(SUNMatrixWrapper &JSparse);
virtual void froot(realtype *root, realtype t, const realtype *x,
const realtype *p, const realtype *k, const realtype *h);
virtual void fxdot(realtype *xdot, realtype t, const realtype *x,
const realtype *p, const realtype *k, const realtype *h,
const realtype *w) = 0;
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);
virtual void fdxdotdp_explicit(realtype *dxdotdp_explicit, realtype t,
const realtype *x, const realtype *p,
const realtype *k, const realtype *h,
const realtype *w);
virtual void fdxdotdp_explicit_colptrs(SUNMatrixWrapper &dxdotdp);
virtual void fdxdotdp_explicit_rowvals(SUNMatrixWrapper &dxdotdp);
virtual void fdxdotdx_explicit(realtype *dxdotdx_explicit, realtype t,
const realtype *x, const realtype *p,
const realtype *k, const realtype *h,
const realtype *w);
virtual void fdxdotdx_explicit_colptrs(SUNMatrixWrapper &dxdotdx);
virtual void fdxdotdx_explicit_rowvals(SUNMatrixWrapper &dxdotdx);
virtual void fdxdotdw(realtype *dxdotdw, realtype t, const realtype *x,
const realtype *p, const realtype *k,
const realtype *h, const realtype *w);
virtual void fdxdotdw_colptrs(SUNMatrixWrapper &dxdotdw);
virtual void fdxdotdw_rowvals(SUNMatrixWrapper &dxdotdw);
void fdxdotdw(realtype t, const_N_Vector x);
void fdxdotdp(realtype t, const_N_Vector x);
void fdxdotdp(realtype t, const AmiVector &x, const AmiVector &dx) override;
};
} // namespace amici
#endif // MODEL_H