src/gromacs/fileio/tngio.h

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  35
  36 #ifndef GMX_FILEIO_TNGIO_H
  37 #define GMX_FILEIO_TNGIO_H
  38
  39 #include <cstdio>
  40
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43 #include "gromacs/utility/real.h"
  44
  45 struct gmx_mtop_t;
  46 struct t_inputrec;
  47 struct gmx_tng_trajectory;
  48 typedef struct gmx_tng_trajectory *gmx_tng_trajectory_t;
  49 struct t_trxframe;
  50
  51 /*! \brief Open a TNG trajectory file
  52  *
  53  * \param filename   Name of file to open
  54  * \param mode       Can be set to 'r', 'w' or 'a' for reading, writing or appending respectively.
  55  * \param tng_data_p Pointer to an allocated gmx_tng_trajectory_t into which a handle to a TNG trajectory will be stored.
  56  *
  57  * Handles all I/O errors internally via fatal error
  58  */
  59 void gmx_tng_open(const char           *filename,
  60                   char                  mode,
  61                   gmx_tng_trajectory_t *tng_data_p);
  62
  63 /*! \brief Finish writing a TNG trajectory file */
  64 void gmx_tng_close(gmx_tng_trajectory_t *tng);
  65
  66 /*!\brief Add molecular topology information to TNG output (if
  67  * available)
  68  *
  69  * \param tng   Valid handle to a TNG trajectory
  70  * \param mtop  Pointer to a topology (can be NULL)
  71  */
  72 void gmx_tng_add_mtop(gmx_tng_trajectory_t  tng,
  73                       const gmx_mtop_t     *mtop);
  74
  75 /*! \brief Do all TNG preparation for full-precision whole-system
  76  * trajectory writing during MD simulations.
  77  *
  78  * \param tng   Valid handle to a TNG trajectory
  79  * \param mtop  Global topology
  80  * \param ir    Input settings (for writing frequencies)
  81  */
  82 void gmx_tng_prepare_md_writing(gmx_tng_trajectory_t  tng,
  83                                 const gmx_mtop_t     *mtop,
  84                                 const t_inputrec     *ir);
  85
  86 /*! \brief Set the default compression precision for TNG writing
  87  *
  88  * \param tng   Valid handle to a TNG trajectory
  89  * \param prec  GROMACS-style precision setting (i.e. 1000 for 3 digits of precision) */
  90 void gmx_tng_set_compression_precision(gmx_tng_trajectory_t tng,
  91                                        real                 prec);
  92
  93 /*! \brief Do all TNG preparation for low-precision selection-based
  94  * trajectory writing during MD simulations.
  95  *
  96  * \param tng   Valid handle to a TNG trajectory
  97  * \param mtop  Global topology
  98  * \param ir    Input settings (for writing frequencies)
  99  */
 100 void gmx_tng_prepare_low_prec_writing(gmx_tng_trajectory_t  tng,
 101                                       const gmx_mtop_t     *mtop,
 102                                       const t_inputrec     *ir);
 103
 104 /*! \brief Write a frame to a TNG file
 105  *
 106  * \param tng                  Valid handle to a TNG trajectory
 107  * \param bUseLossyCompression Whether to use lossy compression
 108  * \param step                 MD step number
 109  * \param elapsedPicoSeconds   Elapsed MD time
 110  * \param lambda               Free-energy lambda value
 111  * \param box                  Simulation box
 112  * \param nAtoms               Number of atoms (i.e. vector lengths)
 113  * \param x                    Vector of position coordinates
 114  * \param v                    Vector of elocities
 115  * \param f                    Vector of forces
 116  *
 117  * The pointers tng, x, v, f may be NULL, which triggers not writing
 118  * (that component). box can only be NULL if x is also NULL. */
 119 void gmx_fwrite_tng(gmx_tng_trajectory_t tng,
 120                     gmx_bool             bUseLossyCompression,
 121                     int64_t              step,
 122                     real                 elapsedPicoSeconds,
 123                     real                 lambda,
 124                     const rvec          *box,
 125                     int                  nAtoms,
 126                     const rvec          *x,
 127                     const rvec          *v,
 128                     const rvec          *f);
 129
 130 /*! \brief Write the current frame set to disk. Perform compression
 131  * etc.
 132  *
 133  * \param tng Valid handle to a TNG trajectory
 134  */
 135 void fflush_tng(gmx_tng_trajectory_t tng);
 136
 137 /*! \brief Get the time (in picoseconds) of the final frame in the
 138  * trajectory.
 139  *
 140  * \param tng Valid handle to a TNG trajectory
 141  */
 142 float gmx_tng_get_time_of_final_frame(gmx_tng_trajectory_t tng);
 143
 144 /*! \brief Prepare to write TNG output from trajectory conversion tools */
 145 void gmx_prepare_tng_writing(const char              *filename,
 146                              char                     mode,
 147                              gmx_tng_trajectory_t    *in,
 148                              gmx_tng_trajectory_t    *out,
 149                              int                      nAtoms,
 150                              const struct gmx_mtop_t *mtop,
 151                              const int               *index,
 152                              const char              *indexGroupName);
 153
 154 /*! \brief Write a trxframe to a TNG file
 155  *
 156  * \param output Trajectory to write to
 157  * \param frame  Frame data to write
 158  * \param natoms Number of atoms to actually write
 159  *
 160  * The natoms field in frame is the number of atoms in the system. The
 161  * parameter natoms supports writing an index-group subset of the
 162  * atoms.
 163  */
 164 void gmx_write_tng_from_trxframe(gmx_tng_trajectory_t    output,
 165                                  const t_trxframe       *frame,
 166                                  int                     natoms);
 167
 168 /*! \brief Creates a molecule containing only the indexed atoms and sets
 169  * the number of all other molecules to 0. Works similar to a
 170  * selection group. */
 171 void gmx_tng_setup_atom_subgroup(gmx_tng_trajectory_t tng,
 172                                  int                  nind,
 173                                  const int           *ind,
 174                                  const char          *name);
 175
 176 /*! \brief Read the first/next TNG frame. */
 177 gmx_bool gmx_read_next_tng_frame(gmx_tng_trajectory_t        input,
 178                                  struct t_trxframe          *fr,
 179                                  int64_t                    *requestedIds,
 180                                  int                         numRequestedIds);
 181
 182 /*! \brief Print the molecule system to stream */
 183 void gmx_print_tng_molecule_system(gmx_tng_trajectory_t input,
 184                                    FILE                *stream);
 185
 186 /*! \brief Get a list of block IDs present in the next frame with data. */
 187 gmx_bool gmx_get_tng_data_block_types_of_next_frame(gmx_tng_trajectory_t input,
 188                                                     int                  frame,
 189                                                     int                  nRequestedIds,
 190                                                     int64_t             *requestedIds,
 191                                                     int64_t             *nextFrame,
 192                                                     int64_t             *nBlocks,
 193                                                     int64_t            **blockIds);
 194
 195 /*! \brief Get data of the next frame with data from the data block
 196  * with the specified block ID. */
 197 gmx_bool gmx_get_tng_data_next_frame_of_block_type(gmx_tng_trajectory_t input,
 198                                                    int64_t              blockId,
 199                                                    real               **values,
 200                                                    int64_t             *frameNumber,
 201                                                    double              *frameTime,
 202                                                    int64_t             *nValuesPerFrame,
 203                                                    int64_t             *nAtoms,
 204                                                    real                *prec,
 205                                                    char                *name,
 206                                                    int                  maxLen,
 207                                                    gmx_bool            *bOK);
 208
 209 /*! \brief Get the output interval of box size.
 210  *
 211  * \return The box output interval, or -1 when TNG support is not available. */
 212 int gmx_tng_get_box_output_interval(gmx_tng_trajectory_t gmx_tng);
 213
 214 /*! \brief Get the output interval of lambda.
 215  *
 216  * \return The box output interval, or -1 when TNG support is not available. */
 217 int gmx_tng_get_lambda_output_interval(gmx_tng_trajectory_t gmx_tng);
 218
 219 #endif /* GMX_FILEIO_TNGIO_H */