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/* The gmx_bools indicate whether a field was read from the trajectory.
 * Do not try to use a pointer when its gmx_bool is FALSE, as memory might
 * not be allocated.
 */
#ifndef GMX_TRAJECTORY_TRX_H
#define GMX_TRAJECTORY_TRX_H

#include <cstdio>

#include <array>

#include "gromacs/math/vectypes.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

struct t_atoms;

typedef struct t_trxframe      // NOLINT (clang-analyzer-optin.performance.Padding)
{
    int             not_ok;    /* integrity flags                  */
    gmx_bool        bDouble;   /* Double precision?                */
    int             natoms;    /* number of atoms (atoms, x, v, f, index) */
    gmx_bool        bStep;
    int64_t         step;      /* MD step number                   */
    gmx_bool        bTime;
    real            time;      /* time of the frame                */
    gmx_bool        bLambda;
    gmx_bool        bFepState; /* does it contain fep_state?       */
    real            lambda;    /* free energy perturbation lambda  */
    int             fep_state; /* which fep state are we in? */
    gmx_bool        bAtoms;
    t_atoms        *atoms;     /* atoms struct (natoms)            */
    gmx_bool        bPrec;
    real            prec;      /* precision of x, fraction of 1 nm */
    gmx_bool        bX;
    rvec           *x;         /* coordinates (natoms)             */
    gmx_bool        bV;
    rvec           *v;         /* velocities (natoms)              */
    gmx_bool        bF;
    rvec           *f;         /* forces (natoms)                  */
    gmx_bool        bBox;
    matrix          box;       /* the 3 box vectors                */
    gmx_bool        bPBC;
    int             ePBC;      /* the type of pbc                  */
    gmx_bool        bIndex;
    int            *index;     /* atom indices of contained coordinates */
} t_trxframe;

void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
                gmx_bool bRMSD, real ftol, real abstol);

void done_frame(t_trxframe *frame);

namespace gmx
{

/*!\brief A 3x3 matrix data type useful for simulation boxes
 *
 * \todo Implement a full replacement for C-style real[DIM][DIM] */
using BoxMatrix = std::array <std::array<real, DIM>, DIM>;

/*! \internal
 * \brief Contains a valid trajectory frame.
 *
 * Valid frames have a step and time, but need not have any particular
 * other fields.
 *
 * \todo Eventually t_trxframe should be replaced by a class such as
 * this. Currently we need to introduce BoxMatrix so that we can have
 * a normal C++ getter that returns the contents of a box matrix,
 * since you cannot use a real[DIM][DIM] as a function return type.
 *
 * \todo Consider a std::optional work-alike type for expressing that
 * a field may or may not have content. */
class TrajectoryFrame
{
    public:
        /*! \brief Constructor
         *
         * \throws APIError If \c frame lacks either step or time.
         */
        explicit TrajectoryFrame(const t_trxframe &frame);
        /*! \brief Return a string that helps users identify this frame, containing time and step number.
         *
         * \throws std::bad_alloc  when out of memory */
        std::string frameName() const;
        //! Step number read from the trajectory file frame.
        std::int64_t step() const;
        //! Time read from the trajectory file frame.
        double time() const;
        //! The PBC characteristics of the box.
        int pbc() const;
        //! Get a view of position coordinates of the frame (which could be empty).
        ArrayRef<const RVec> x() const;
        //! Get a view of velocity coordinates of the frame (which could be empty).
        ArrayRef<const RVec> v() const;
        //! Get a view of force coordinates of the frame (which could be empty).
        ArrayRef<const RVec> f() const;
        //! Return whether the frame has a box.
        bool hasBox() const;
        //! Return a handle to the frame's box, which is all zero if the frame has no box.
        const BoxMatrix &box() const;
    private:
        //! Handle to trajectory data
        const t_trxframe &frame_;
        //! Box matrix data from the frame_.
        BoxMatrix         box_;
};

} // namespace gmx

#endif
