libgromacs-dev 2018.1-1 / usr / include / gromacs / fileio / trrio.h

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#ifndef GMX_FILEIO_TRRIO_H
#define GMX_FILEIO_TRRIO_H

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

/**************************************************************
 *
 * These routines handle trr (trajectory) I/O, they read and
 * write trr files. The routines should be able to read single
 * and double precision files without the user noting it.
 * The files are backward compatible, therefore the header holds
 * some unused variables.
 *
 * The routines in the corresponding c-file trrio.cpp
 * are based on the lower level routines in gmxfio.cpp
 * The file handle returned from gmx_trr_open()
 * can also be used with the routines in gmxfio.h
 *
 * Note that TRR was designed to represent a step number as a default
 * integer, which depends on the implementation, but is typically and
 * 32 bit. We didn't design the format to be extensible, so we can't
 * fix the fact that after 2^31 frames, step numbers will wrap to be
 * negative. Fortunately, this tends not to cause serious problems,
 * and we've fixed it in TNG. Meanwhile, the implementation pretends
 * to the rest of GROMACS that it functions with gmx_int64_t like all
 * other step numbers, but the actual range in practice depends on the
 * defaults of the implementation in use now (or when the file was
 * written).
 *
 **************************************************************/

#ifdef __cplusplus
extern "C" {
#endif

struct t_fileio;

/* This struct describes the order and the  */
/* sizes of the structs in a trr file, sizes are given in bytes. */
typedef struct gmx_trr_header_t
{
    gmx_bool    bDouble;   /* Double precision?                   */
    int         ir_size;   /* Backward compatibility              */
    int         e_size;    /* Backward compatibility              */
    int         box_size;  /* Non zero if a box is present        */
    int         vir_size;  /* Backward compatibility              */
    int         pres_size; /* Backward compatibility              */
    int         top_size;  /* Backward compatibility              */
    int         sym_size;  /* Backward compatibility              */
    int         x_size;    /* Non zero if coordinates are present */
    int         v_size;    /* Non zero if velocities are present  */
    int         f_size;    /* Non zero if forces are present      */

    int         natoms;    /* The total number of atoms           */
    gmx_int64_t step;      /* Current step number                 */
    int         nre;       /* Backward compatibility              */
    real        t;         /* Current time                        */
    real        lambda;    /* Current value of lambda             */
    int         fep_state; /* Current value of alchemical state   */
} gmx_trr_header_t;

struct t_fileio *gmx_trr_open(const char *fn, const char *mode);
/* Open a trr file */

void gmx_trr_close(struct t_fileio *fio);
/* Close it */

gmx_bool gmx_trr_read_frame_header(struct t_fileio *fio, gmx_trr_header_t *header, gmx_bool *bOK);
/* Read the header of a trr file. Return FALSE if there is no frame.
 * bOK will be FALSE when the header is incomplete.
 */

gmx_bool gmx_trr_read_frame_data(struct t_fileio *fio, gmx_trr_header_t *sh,
                                 rvec *box, rvec *x, rvec *v, rvec *f);
/* Extern read a frame except the header (that should be pre-read,
 * using routine gmx_trr_read_frame_header(), see above) from a trr file.
 * Return FALSE on error
 */

gmx_bool gmx_trr_read_frame(struct t_fileio *fio, gmx_int64_t *step, real *t, real *lambda,
                            rvec *box, int *natoms, rvec *x, rvec *v, rvec *f);
/* Read a trr frame, including the header from fp. box, x, v, f may
 * be NULL, in which case the data will be skipped over.
 * return FALSE on error
 */

void gmx_trr_write_frame(struct t_fileio *fio, gmx_int64_t step, real t, real lambda,
                         const rvec *box, int natoms, const rvec *x, const rvec *v, const rvec *f);
/* Write a trr frame to file fp, box, x, v, f may be NULL */

void gmx_trr_read_single_header(const char *fn, gmx_trr_header_t *header);
/* Read the header of a trr file from fn, and close the file afterwards.
 */

void gmx_trr_read_single_frame(const char *fn, gmx_int64_t *step, real *t, real *lambda,
                               rvec *box, int *natoms, rvec *x, rvec *v, rvec *f);
/* Read a single trr frame from file fn, which is closed afterwards
 */

void gmx_trr_write_single_frame(const char *fn, gmx_int64_t step, real t, real lambda,
                                const rvec *box, int natoms, const rvec *x, const rvec *v, const rvec *f);
/* Write a single trr frame to file fn, which is closed afterwards */

#ifdef __cplusplus
}
#endif


#endif