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#ifndef GMX_FILEIO_TNGIO_H
#define GMX_FILEIO_TNGIO_H

#include <cstdio>

#include <filesystem>

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

struct gmx_mtop_t;
struct t_inputrec;
struct gmx_tng_trajectory;
typedef struct gmx_tng_trajectory* gmx_tng_trajectory_t;
struct t_trxframe;

namespace gmx
{
template<typename>
class ArrayRef;
}
/*! \brief Open a TNG trajectory file
 *
 * \param filename   Name of file to open
 * \param mode       Can be set to 'r', 'w' or 'a' for reading, writing or appending respectively.
 * \param tng_data_p Pointer to an allocated gmx_tng_trajectory_t into which a handle to a TNG trajectory will be stored.
 *
 * Handles all I/O errors internally via fatal error
 */
void gmx_tng_open(const std::filesystem::path& filename, char mode, gmx_tng_trajectory_t* tng_data_p);

/*! \brief Finish writing a TNG trajectory file */
void gmx_tng_close(gmx_tng_trajectory_t* tng);

/*!\brief Add molecular topology information to TNG output (if
 * available)
 *
 * \param tng   Valid handle to a TNG trajectory
 * \param mtop  Pointer to a topology (can be NULL)
 */
void gmx_tng_add_mtop(gmx_tng_trajectory_t tng, const gmx_mtop_t* mtop);

/*! \brief Do all TNG preparation for full-precision whole-system
 * trajectory writing during MD simulations.
 *
 * \param tng   Valid handle to a TNG trajectory
 * \param mtop  Global topology
 * \param ir    Input settings (for writing frequencies)
 */
void gmx_tng_prepare_md_writing(gmx_tng_trajectory_t tng, const gmx_mtop_t* mtop, const t_inputrec* ir);

/*! \brief Set the default compression precision for TNG writing
 *
 * \param tng   Valid handle to a TNG trajectory
 * \param prec  GROMACS-style precision setting (i.e. 1000 for 3 digits of precision) */
void gmx_tng_set_compression_precision(gmx_tng_trajectory_t tng, real prec);

/*! \brief Do all TNG preparation for low-precision selection-based
 * trajectory writing during MD simulations.
 *
 * \param tng   Valid handle to a TNG trajectory
 * \param mtop  Global topology
 * \param ir    Input settings (for writing frequencies)
 */
void gmx_tng_prepare_low_prec_writing(gmx_tng_trajectory_t tng, const gmx_mtop_t* mtop, const t_inputrec* ir);

/*! \brief Write a frame to a TNG file
 *
 * \param tng                  Valid handle to a TNG trajectory
 * \param bUseLossyCompression Whether to use lossy compression
 * \param step                 MD step number
 * \param elapsedPicoSeconds   Elapsed MD time
 * \param lambda               Free-energy lambda value
 * \param box                  Simulation box
 * \param nAtoms               Number of atoms (i.e. vector lengths)
 * \param x                    Vector of position coordinates
 * \param v                    Vector of elocities
 * \param f                    Vector of forces
 *
 * The pointers tng, x, v, f may be NULL, which triggers not writing
 * (that component). box can only be NULL if x is also NULL. */
void gmx_fwrite_tng(gmx_tng_trajectory_t tng,
                    gmx_bool             bUseLossyCompression,
                    int64_t              step,
                    real                 elapsedPicoSeconds,
                    real                 lambda,
                    const rvec*          box,
                    int                  nAtoms,
                    const rvec*          x,
                    const rvec*          v,
                    const rvec*          f);

/*! \brief Write the current frame set to disk. Perform compression
 * etc.
 *
 * \param tng Valid handle to a TNG trajectory
 */
void fflush_tng(gmx_tng_trajectory_t tng);

/*! \brief Get the time (in picoseconds) of the final frame in the
 * trajectory.
 *
 * \param tng Valid handle to a TNG trajectory
 */
float gmx_tng_get_time_of_final_frame(gmx_tng_trajectory_t tng);

/*! \brief Prepare to write TNG output from trajectory conversion tools */
void gmx_prepare_tng_writing(const std::filesystem::path& filename,
                             char                         mode,
                             gmx_tng_trajectory_t*        in,
                             gmx_tng_trajectory_t*        out,
                             int                          nAtoms,
                             const struct gmx_mtop_t*     mtop,
                             gmx::ArrayRef<const int>     index,
                             const char*                  indexGroupName);

/*! \brief Write a trxframe to a TNG file
 *
 * \param output Trajectory to write to
 * \param frame  Frame data to write
 * \param natoms Number of atoms to actually write
 *
 * The natoms field in frame is the number of atoms in the system. The
 * parameter natoms supports writing an index-group subset of the
 * atoms.
 */
void gmx_write_tng_from_trxframe(gmx_tng_trajectory_t output, const t_trxframe* frame, int natoms);

/*! \brief Creates a molecule containing only the indexed atoms and sets
 * the number of all other molecules to 0. Works similar to a
 * selection group. */
void gmx_tng_setup_atom_subgroup(gmx_tng_trajectory_t tng, gmx::ArrayRef<const int> ind, const char* name);

/*! \brief Read the first/next TNG frame. */
gmx_bool gmx_read_next_tng_frame(gmx_tng_trajectory_t input,
                                 struct t_trxframe*   fr,
                                 int64_t*             requestedIds,
                                 int                  numRequestedIds);

/*! \brief Print the molecule system to stream */
void gmx_print_tng_molecule_system(gmx_tng_trajectory_t input, FILE* stream);

/*! \brief Get a list of block IDs present in the next frame with data. */
gmx_bool gmx_get_tng_data_block_types_of_next_frame(gmx_tng_trajectory_t input,
                                                    int                  frame,
                                                    int                  nRequestedIds,
                                                    int64_t*             requestedIds,
                                                    int64_t*             nextFrame,
                                                    int64_t*             nBlocks,
                                                    int64_t**            blockIds);

/*! \brief Get data of the next frame with data from the data block
 * with the specified block ID. */
gmx_bool gmx_get_tng_data_next_frame_of_block_type(gmx_tng_trajectory_t input,
                                                   int64_t              blockId,
                                                   real**               values,
                                                   int64_t*             frameNumber,
                                                   double*              frameTime,
                                                   int64_t*             nValuesPerFrame,
                                                   int64_t*             nAtoms,
                                                   real*                prec,
                                                   char*                name,
                                                   int                  maxLen,
                                                   gmx_bool*            bOK);

/*! \brief Get the output interval of box size.
 *
 * \return The box output interval, or -1 when TNG support is not available. */
int gmx_tng_get_box_output_interval(gmx_tng_trajectory_t gmx_tng);

/*! \brief Get the output interval of lambda.
 *
 * \return The box output interval, or -1 when TNG support is not available. */
int gmx_tng_get_lambda_output_interval(gmx_tng_trajectory_t gmx_tng);

#endif /* GMX_FILEIO_TNGIO_H */
