Program Listing for File abstract_model.h

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#ifndef AMICI_ABSTRACT_MODEL_H
#define AMICI_ABSTRACT_MODEL_H

#include "amici/defines.h"
#include "amici/splinefunctions.h"
#include "amici/sundials_matrix_wrapper.h"
#include "amici/vector.h"

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

#include <memory>

namespace amici {

class Solver;

class AbstractModel {
  public:
    virtual ~AbstractModel() = default;

    virtual std::unique_ptr<Solver> getSolver() = 0;

    virtual void froot(
        realtype const t, AmiVector const& x, AmiVector const& dx,
        gsl::span<realtype> root
    ) = 0;

    virtual void fxdot(
        realtype const t, AmiVector const& x, AmiVector const& dx,
        AmiVector& xdot
    ) = 0;

    virtual void fsxdot(
        realtype const t, AmiVector const& x, AmiVector const& dx, int ip,
        AmiVector const& sx, AmiVector const& sdx, AmiVector& sxdot
    ) = 0;

    virtual void fxBdot_ss(
        realtype const t, AmiVector const& xB, AmiVector const& dxB,
        AmiVector& xBdot
    ) = 0;

    virtual void fJSparseB_ss(SUNMatrix JB) = 0;

    virtual void writeSteadystateJB(
        realtype const t, realtype cj, AmiVector const& x, AmiVector const& dx,
        AmiVector const& xB, AmiVector const& dxB, AmiVector const& xBdot
    ) = 0;

    virtual void
    fJ(realtype const t, realtype cj, AmiVector const& x, AmiVector const& dx,
       AmiVector const& xdot, SUNMatrix J)
        = 0;

    virtual void
    fJB(realtype const t, realtype cj, AmiVector const& x, AmiVector const& dx,
        AmiVector const& xB, AmiVector const& dxB, AmiVector const& xBdot,
        SUNMatrix JB)
        = 0;

    virtual void fJSparse(
        realtype const t, realtype cj, AmiVector const& x, AmiVector const& dx,
        AmiVector const& xdot, SUNMatrix J
    ) = 0;

    virtual void fJSparseB(
        realtype const t, realtype cj, AmiVector const& x, AmiVector const& dx,
        AmiVector const& xB, AmiVector const& dxB, AmiVector const& xBdot,
        SUNMatrix JB
    ) = 0;

    virtual void fJDiag(
        realtype const t, AmiVector& Jdiag, realtype cj, AmiVector const& x,
        AmiVector const& dx
    ) = 0;

    virtual void
    fdxdotdp(realtype const t, AmiVector const& x, AmiVector const& dx)
        = 0;

    virtual void
    fJv(realtype const t, AmiVector const& x, AmiVector const& dx,
        AmiVector const& xdot, AmiVector const& v, AmiVector& nJv, realtype cj)
        = 0;

    virtual std::string getAmiciVersion() const;

    virtual std::string getAmiciCommit() const;

    virtual void
    fx0(realtype* x0, realtype const t, realtype const* p, realtype const* k);

    virtual bool isFixedParameterStateReinitializationAllowed() const;

    virtual void fx0_fixedParameters(
        realtype* x0, realtype const t, realtype const* p, realtype const* k,
        gsl::span<int const> reinitialization_state_idxs
    );

    virtual void fsx0_fixedParameters(
        realtype* sx0, realtype const t, realtype const* x0, realtype const* p,
        realtype const* k, int ip,
        gsl::span<int const> reinitialization_state_idxs
    );

    virtual void fsx0(
        realtype* sx0, realtype const t, realtype const* x0, realtype const* p,
        realtype const* k, int ip
    );

    virtual void fdx0(AmiVector& x0, AmiVector& dx0);

    virtual void fstau(
        realtype* stau, realtype const t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, realtype const* tcl,
        realtype const* sx, int ip, int ie
    );

    virtual void
    fy(realtype* y, realtype const t, realtype const* x, realtype const* p,
       realtype const* k, realtype const* h, realtype const* w);

    virtual void fdydp(
        realtype* dydp, realtype const t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, int ip, realtype const* w,
        realtype const* dwdp
    );

    virtual void fdydp(
        realtype* dydp, realtype const t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, int ip, realtype const* w,
        realtype const* tcl, realtype const* dtcldp, realtype const* spl,
        realtype const* sspl
    );

    virtual void fdydx(
        realtype* dydx, realtype const t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, realtype const* w,
        realtype const* dwdx
    );

    virtual void
    fz(realtype* z, int ie, realtype const t, realtype const* x,
       realtype const* p, realtype const* k, realtype const* h);

    virtual void
    fsz(realtype* sz, int ie, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h,
        realtype const* sx, int ip);

    virtual void
    frz(realtype* rz, int ie, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h);

    virtual void fsrz(
        realtype* srz, int ie, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h,
        realtype const* sx, int ip
    );

    virtual void fdzdp(
        realtype* dzdp, int ie, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h, int ip
    );

    virtual void fdzdx(
        realtype* dzdx, int ie, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h
    );

    virtual void fdrzdp(
        realtype* drzdp, int ie, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h, int ip
    );

    virtual void fdrzdx(
        realtype* drzdx, int ie, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h
    );

    virtual void fdeltax(
        realtype* deltax, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h, int ie,
        realtype const* xdot, realtype const* xdot_old
    );

    virtual void fdeltasx(
        realtype* deltasx, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h,
        realtype const* w, int ip, int ie, realtype const* xdot,
        realtype const* xdot_old, realtype const* sx, realtype const* stau,
        realtype const* tcl
    );

    virtual void fdeltaxB(
        realtype* deltaxB, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h, int ie,
        realtype const* xdot, realtype const* xdot_old, realtype const* xB
    );

    virtual void fdeltaqB(
        realtype* deltaqB, realtype const t, realtype const* x,
        realtype const* p, realtype const* k, realtype const* h, int ip, int ie,
        realtype const* xdot, realtype const* xdot_old, realtype const* xB
    );

    virtual void fsigmay(
        realtype* sigmay, realtype const t, realtype const* p,
        realtype const* k, realtype const* y
    );

    virtual void fdsigmaydp(
        realtype* dsigmaydp, realtype const t, realtype const* p,
        realtype const* k, realtype const* y, int ip
    );
    virtual void fdsigmaydy(
        realtype* dsigmaydy, realtype const t, realtype const* p,
        realtype const* k, realtype const* y
    );

    virtual void fsigmaz(
        realtype* sigmaz, realtype const t, realtype const* p, realtype const* k
    );

    virtual void fdsigmazdp(
        realtype* dsigmazdp, realtype const t, realtype const* p,
        realtype const* k, int ip
    );

    virtual void
    fJy(realtype* nllh, int iy, realtype const* p, realtype const* k,
        realtype const* y, realtype const* sigmay, realtype const* my);

    virtual void
    fJz(realtype* nllh, int iz, realtype const* p, realtype const* k,
        realtype const* z, realtype const* sigmaz, realtype const* mz);

    virtual void fJrz(
        realtype* nllh, int iz, realtype const* p, realtype const* k,
        realtype const* z, realtype const* sigmaz
    );

    virtual void fdJydy(
        realtype* dJydy, int iy, realtype const* p, realtype const* k,
        realtype const* y, realtype const* sigmay, realtype const* my
    );

    virtual void fdJydy_colptrs(SUNMatrixWrapper& dJydy, int index);

    virtual void fdJydy_rowvals(SUNMatrixWrapper& dJydy, int index);

    virtual void fdJydsigma(
        realtype* dJydsigma, int iy, realtype const* p, realtype const* k,
        realtype const* y, realtype const* sigmay, realtype const* my
    );

    virtual void fdJzdz(
        realtype* dJzdz, int iz, realtype const* p, realtype const* k,
        realtype const* z, realtype const* sigmaz, realtype const* mz
    );

    virtual void fdJzdsigma(
        realtype* dJzdsigma, int iz, realtype const* p, realtype const* k,
        realtype const* z, realtype const* sigmaz, realtype const* mz
    );

    virtual void fdJrzdz(
        realtype* dJrzdz, int iz, realtype const* p, realtype const* k,
        realtype const* rz, realtype const* sigmaz
    );

    virtual void fdJrzdsigma(
        realtype* dJrzdsigma, int iz, realtype const* p, realtype const* k,
        realtype const* rz, realtype const* sigmaz
    );

    virtual void
    fw(realtype* w, realtype const t, realtype const* x, realtype const* p,
       realtype const* k, realtype const* h, realtype const* tcl,
       realtype const* spl, bool include_static = true);

    virtual void fdwdp(
        realtype* dwdp, realtype const t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, realtype const* w,
        realtype const* tcl, realtype const* stcl, realtype const* spl,
        realtype const* sspl, bool include_static = true
    );

    virtual void fdwdp_colptrs(SUNMatrixWrapper& dwdp);

    virtual void fdwdp_rowvals(SUNMatrixWrapper& dwdp);

    virtual void fdwdx(
        realtype* dwdx, realtype const t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, realtype const* w,
        realtype const* tcl, realtype const* spl, bool include_static = true
    );

    virtual void fdwdx_colptrs(SUNMatrixWrapper& dwdx);

    virtual void fdwdx_rowvals(SUNMatrixWrapper& dwdx);

    virtual void fdwdw(
        realtype* dwdw, realtype t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, realtype const* w,
        realtype const* tcl, bool include_static = true
    );

    virtual void fdwdw_colptrs(SUNMatrixWrapper& dwdw);

    virtual void fdwdw_rowvals(SUNMatrixWrapper& dwdw);

    virtual void fdx_rdatadx_solver(
        realtype* dx_rdatadx_solver, realtype const* x, realtype const* tcl,
        realtype const* p, realtype const* k
    );

    virtual void fdx_rdatadx_solver_colptrs(SUNMatrixWrapper& dxrdatadxsolver);

    virtual void fdx_rdatadx_solver_rowvals(SUNMatrixWrapper& dxrdatadxsolver);

    virtual void fdx_rdatadp(
        realtype* dx_rdatadp, realtype const* x, realtype const* tcl,
        realtype const* p, realtype const* k, int const ip
    );

    virtual void fdx_rdatadtcl(
        realtype* dx_rdatadtcl, realtype const* x, realtype const* tcl,
        realtype const* p, realtype const* k
    );

    virtual void fdx_rdatadtcl_colptrs(SUNMatrixWrapper& dx_rdatadtcl);

    virtual void fdx_rdatadtcl_rowvals(SUNMatrixWrapper& dx_rdatadtcl);

    virtual void fdtotal_cldp(
        realtype* dtotal_cldp, realtype const* x_rdata, realtype const* p,
        realtype const* k, int const ip
    );

    virtual void fdtotal_cldx_rdata(
        realtype* dtotal_cldx_rdata, realtype const* x_rdata, realtype const* p,
        realtype const* k, realtype const* tcl
    );

    virtual void fdtotal_cldx_rdata_colptrs(SUNMatrixWrapper& dtotal_cldx_rdata
    );

    virtual void fdtotal_cldx_rdata_rowvals(SUNMatrixWrapper& dtotal_cldx_rdata
    );

    virtual std::vector<HermiteSpline>
    fcreate_splines(realtype const* p, realtype const* k);

    virtual void fdspline_valuesdp(
        realtype* dspline_valuesdp, realtype const* p, realtype const* k,
        int const ip
    );

    virtual void fdspline_slopesdp(
        realtype* dspline_slopesdp, realtype const* p, realtype const* k,
        int const ip
    );
};

} // namespace amici

#endif // AMICI_ABSTRACT_MODEL_H