Program Listing for File model_dae.h

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#ifndef AMICI_MODEL_DAE_H
#define AMICI_MODEL_DAE_H

#include "amici/model.h"

#include <nvector/nvector_serial.h>

#include <sunmatrix/sunmatrix_band.h>
#include <sunmatrix/sunmatrix_dense.h>
#include <sunmatrix/sunmatrix_sparse.h>

#include <utility>
#include <vector>

namespace amici {

class ExpData;
class IDASolver;

class Model_DAE : public Model {
  public:
    Model_DAE() = default;

    Model_DAE(const ModelDimensions &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)
        : Model(model_dimensions, simulation_parameters,
                o2mode, idlist, z2event, pythonGenerated,
                ndxdotdp_explicit) {
        derived_state_.M_ = SUNMatrixWrapper(nx_solver, nx_solver);
    }

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

    void fJ(realtype t, realtype cj, const_N_Vector x, const_N_Vector dx,
            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, realtype cj, const_N_Vector x, const_N_Vector dx,
             const_N_Vector xB, const_N_Vector dxB, SUNMatrix JB);

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

    void fJSparse(realtype t, realtype cj, const_N_Vector x, const_N_Vector dx,
                  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, realtype cj, const_N_Vector x, const_N_Vector dx,
                   const_N_Vector xB, const_N_Vector dxB, SUNMatrix JB);

    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(realtype t, const_N_Vector x, const_N_Vector dx, const_N_Vector v,
             N_Vector Jv, realtype cj);

    void fJvB(realtype t, const_N_Vector x, const_N_Vector dx,
              const_N_Vector xB, const_N_Vector dxB,
              const_N_Vector vB, N_Vector JvB, realtype cj);

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

    void froot(realtype t, const_N_Vector x, const_N_Vector dx, 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, const_N_Vector dx, N_Vector xdot);

    void fxBdot(realtype t, const_N_Vector x, const_N_Vector dx,
                const_N_Vector xB, const_N_Vector dxB, N_Vector xBdot);

    void fqBdot(realtype t, const_N_Vector x, const_N_Vector dx,
                const_N_Vector xB, const_N_Vector dxB,
                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, const_N_Vector dxB,
                   N_Vector xBdot) const;

    void fqBdot_ss(realtype t, const_N_Vector xB, const_N_Vector dxB,
                   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 fdxdotdp(realtype t, const const_N_Vector x, const const_N_Vector dx);
    void fdxdotdp(const realtype t, const AmiVector &x,
                  const AmiVector &dx) override {
        fdxdotdp(t, x.getNVector(), dx.getNVector());
    };

    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, const_N_Vector dx, int ip,
                const_N_Vector sx, const_N_Vector sdx, N_Vector sxdot);

    void fM(realtype t, const_N_Vector x);

    std::unique_ptr<Solver> getSolver() override;

  protected:
    virtual void fJSparse(SUNMatrixContent_Sparse JSparse, realtype t,
                          const realtype *x, const double *p, const double *k,
                          const realtype *h, realtype cj, const realtype *dx,
                          const realtype *w, const realtype *dwdx) = 0;

    virtual void froot(realtype *root, realtype t, const realtype *x,
                       const double *p, const double *k, const realtype *h,
                       const realtype *dx);

    virtual void fxdot(realtype *xdot, realtype t, const realtype *x,
                       const double *p, const double *k, const realtype *h,
                       const realtype *dx, 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 *dx,
                          const realtype *w, const realtype *dwdp);

    virtual void fM(realtype *M, const realtype t, const realtype *x,
                    const realtype *p, const realtype *k);
};
} // namespace amici

#endif // MODEL_H