src/gromacs/fileio/trxio.h

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  37
  38 #ifndef GMX_FILEIO_TRXIO_H
  39 #define GMX_FILEIO_TRXIO_H
  40
  41 #include "gromacs/fileio/pdbio.h"
  42 #include "gromacs/utility/arrayref.h"
  43
  44 struct gmx_mtop_t;
  45 struct gmx_output_env_t;
  46 struct t_atoms;
  47 struct t_fileio;
  48 struct t_topology;
  49 struct t_trxframe;
  50
  51 /* a dedicated status type contains fp, etc. */
  52 typedef struct t_trxstatus t_trxstatus;
  53
  54 /* I/O function types */
  55
  56 /************************************************
  57  *             Trajectory functions
  58  ************************************************/
  59
  60 int prec2ndec(real prec);
  61 /* Convert precision in 1/(nm) to number of decimal places */
  62
  63 /*! \brief Convert number of decimal places to trajectory precision in
  64  * 1/(nm) */
  65 real ndec2prec(int ndec);
  66
  67 void clear_trxframe(struct t_trxframe* fr, gmx_bool bFirst);
  68 /* Set all content gmx_booleans to FALSE.
  69  * When bFirst = TRUE, set natoms=-1, all pointers to NULL
  70  *                     and all data to zero.
  71  */
  72
  73 void set_trxframe_ePBC(struct t_trxframe* fr, int ePBC);
  74 /* Set the type of periodic boundary conditions, ePBC=-1 is not set */
  75
  76 int nframes_read(t_trxstatus* status);
  77 /* Returns the number of frames read from the trajectory */
  78
  79 int write_trxframe_indexed(t_trxstatus* status, const t_trxframe* fr, int nind, const int* ind, gmx_conect gc);
  80 /* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */
  81
  82 int write_trxframe(t_trxstatus* status, struct t_trxframe* fr, gmx_conect gc);
  83 /* Write a frame to a TRX file.
  84  * Only entries for which the gmx_boolean is TRUE will be written,
  85  * except for step, time, lambda and/or box, which may not be
  86  * omitted for certain trajectory formats.
  87  * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
  88  * the precision is set to 1000.
  89  * gc is important for pdb file writing only and may be NULL.
  90  */
  91
  92 int write_trx(t_trxstatus*   status,
  93               int            nind,
  94               const int*     ind,
  95               const t_atoms* atoms,
  96               int            step,
  97               real           time,
  98               matrix         box,
  99               rvec           x[],
 100               rvec*          v,
 101               gmx_conect     gc);
 102 /* Write an indexed frame to a TRX file.
 103  * v can be NULL.
 104  * atoms can be NULL for file types which don't need atom names.
 105  */
 106
 107 /*! \brief
 108  * Set up TNG writing to \p out.
 109  *
 110  * Sets up \p out for writing TNG. If \p in != NULL and contains a TNG trajectory
 111  * some data, e.g. molecule system, will be copied over from \p in to the return value.
 112  * If \p in == NULL a file name (infile) of a TNG file can be provided instead
 113  * and used for copying data to the return value.
 114  * If there is no TNG input \p natoms is used to create "implicit atoms" (no atom
 115  * or molecular data present). If \p natoms == -1 the number of atoms are
 116  * not known (or there is already a TNG molecule system to copy, in which case
 117  * natoms is not required anyhow). If an group of indexed atoms are written
 118  * \p natoms must be the length of \p index. \p index_group_name is the name of the
 119  * index group.
 120  *
 121  * \param[in] filename Name of new TNG file.
 122  * \param[in] filemode How to open the output file.
 123  * \param[in] in Input file pointer or null.
 124  * \param[in] infile Input file name or null.
 125  * \param[in] natoms Number of atoms to write.
 126  * \param[in] mtop Pointer to system topology or null.
 127  * \param[in] index Array of atom indices.
 128  * \param[in] index_group_name Name of the group of atom indices.
 129  * \returns Pointer to output TNG file.
 130  */
 131 t_trxstatus* trjtools_gmx_prepare_tng_writing(const char*              filename,
 132                                               char                     filemode,
 133                                               t_trxstatus*             in,
 134                                               const char*              infile,
 135                                               int                      natoms,
 136                                               const struct gmx_mtop_t* mtop,
 137                                               gmx::ArrayRef<const int> index,
 138                                               const char*              index_group_name);
 139
 140 /*! \brief Write a trxframe to the TNG file in status.
 141  *
 142  * This function is needed because both t_trxstatus and
 143  * gmx_tng_trajectory_t are encapsulated, so client trajectory-writing
 144  * code with a t_trxstatus can't just call the TNG writing
 145  * function. */
 146 void write_tng_frame(t_trxstatus* status, struct t_trxframe* fr);
 147
 148 void close_trx(t_trxstatus* status);
 149 /* Close trajectory file as opened with read_first_x, read_first_frame
 150  * or open_trx.
 151  * Also frees memory in the structure.
 152  */
 153
 154 t_trxstatus* open_trx(const char* outfile, const char* filemode);
 155 /* Open a TRX file and return an allocated status pointer */
 156
 157 struct t_fileio* trx_get_fileio(t_trxstatus* status);
 158 /* get a fileio from a trxstatus */
 159
 160 float trx_get_time_of_final_frame(t_trxstatus* status);
 161 /* get time of final frame. Only supported for TNG and XTC */
 162
 163 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble);
 164 /* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
 165  * larger than the float/double precision.
 166  */
 167
 168 #if GMX_DOUBLE
 169 #    define bRmod(a, b, c) bRmod_fd(a, b, c, TRUE)
 170 #else
 171 #    define bRmod(a, b, c) bRmod_fd(a, b, c, FALSE)
 172 #endif
 173
 174 int check_times2(real t, real t0, gmx_bool bDouble);
 175 /* This routine checkes if the read-in time is correct or not;
 176  * returns -1 if t<tbegin or t MOD dt = t0,
 177  *          0 if tbegin <= t <=tend+margin,
 178  *          1 if t>tend
 179  * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
 180  * tp and tpp should be the time of the previous frame and the one before.
 181  * The mod is done with single or double precision accuracy depending
 182  * on the value of bDouble.
 183  */
 184
 185 int check_times(real t);
 186 /* This routine checkes if the read-in time is correct or not;
 187  * returns -1 if t<tbegin,
 188  *          0 if tbegin <= t <=tend,
 189  *          1 if t>tend
 190  */
 191
 192
 193 /* For trxframe.flags, used in trxframe read routines.
 194  * When a READ flag is set, the field will be read when present,
 195  * but a frame might be returned which does not contain the field.
 196  * When a NEED flag is set, frames not containing the field will be skipped.
 197  */
 198 #define TRX_READ_X (1u << 0u)
 199 #define TRX_NEED_X (1u << 1u)
 200 #define TRX_READ_V (1u << 2u)
 201 #define TRX_NEED_V (1u << 3u)
 202 #define TRX_READ_F (1u << 4u)
 203 #define TRX_NEED_F (1u << 5u)
 204 /* Useful for reading natoms from a trajectory without skipping */
 205 #define TRX_DONT_SKIP (1u << 6u)
 206
 207 /* For trxframe.not_ok */
 208 #define HEADER_NOT_OK (1u << 0u)
 209 #define DATA_NOT_OK (1u << 1u)
 210 #define FRAME_NOT_OK (HEADER_NOT_OK | DATA_NOT_OK)
 211
 212 bool read_first_frame(const gmx_output_env_t* oenv,
 213                       t_trxstatus**           status,
 214                       const char*             fn,
 215                       struct t_trxframe*      fr,
 216                       int                     flags);
 217 /* Read the first frame which is in accordance with flags, which are
 218  * defined further up in this file.
 219  * Memory will be allocated for flagged entries.
 220  * The flags are copied to fr for subsequent calls to read_next_frame.
 221  * Returns true when succeeded, false otherwise.
 222  */
 223
 224 bool read_next_frame(const gmx_output_env_t* oenv, t_trxstatus* status, struct t_trxframe* fr);
 225 /* Reads the next frame which is in accordance with fr->flags.
 226  * Returns true when succeeded, false otherwise.
 227  */
 228
 229 int read_first_x(const gmx_output_env_t* oenv, t_trxstatus** status, const char* fn, real* t, rvec** x, matrix box);
 230 /* These routines read first coordinates and box, and allocates
 231  * memory for the coordinates, for a trajectory file.
 232  * The routine returns the number of atoms, or 0 when something is wrong.
 233  * The integer in status should be passed to calls of read_next_x
 234  */
 235
 236 gmx_bool read_next_x(const gmx_output_env_t* oenv, t_trxstatus* status, real* t, rvec x[], matrix box);
 237 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
 238  * or FALSE when end of file (or last frame requested by user).
 239  * status is the integer set in read_first_x.
 240  */
 241
 242 void rewind_trj(t_trxstatus* status);
 243 /* Rewind trajectory file as opened with read_first_x */
 244
 245 struct t_topology* read_top(const char* fn, int* ePBC);
 246 /* Extract a topology data structure from a topology file.
 247  * If ePBC!=NULL *ePBC gives the pbc type.
 248  */
 249
 250 #endif