gromacs-dev 4.6.5-1build1 / usr / include / gromacs / position.h

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/*! \file
 * \brief API for handling positions.
 */
#ifndef POSITION_H
#define POSITION_H

#include "typedefs.h"

#include "indexutil.h"

#ifdef __cplusplus
extern "C" {
#endif

/*! \brief
 * Stores a set of positions together with their origins.
 */
typedef struct gmx_ana_pos_t
{
    /*! \brief
     * Number of positions.
     */
    int                 nr;
    /*! \brief
     * Array of positions.
     */
    rvec               *x;
    /*! \brief
     * Velocities (can be NULL).
     */
    rvec               *v;
    /*! \brief
     * Forces (can be NULL).
     */
    rvec               *f;
    /*! \brief
     * Mapping of the current positions to the original group.
     *
     * \see gmx_ana_indexmap_t
     */
    gmx_ana_indexmap_t  m;
    /*! \brief
     * Pointer to the current evaluation group.
     */
    gmx_ana_index_t    *g;
    /*! \brief
     * Number of elements allocated for \c x.
     */
    int                 nalloc_x;
} gmx_ana_pos_t;

/** Initializes an empty position structure. */
void
gmx_ana_pos_clear(gmx_ana_pos_t *pos);
/** Ensures that enough memory has been allocated to store positions. */
void
gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize);
/** Request memory allocation for velocities. */
void
gmx_ana_pos_reserve_velocities(gmx_ana_pos_t *pos);
/** Request memory allocation for forces. */
void
gmx_ana_pos_reserve_forces(gmx_ana_pos_t *pos);
/** Initializes a \c gmx_ana_pos_t to represent a constant position. */
void
gmx_ana_pos_init_const(gmx_ana_pos_t *pos, rvec x);
/** Frees the memory allocated for position storage. */
void
gmx_ana_pos_deinit(gmx_ana_pos_t *pos);
/** Frees the memory allocated for positions. */
void
gmx_ana_pos_free(gmx_ana_pos_t *pos);
/** Copies the evaluated positions to a preallocated data structure. */
void
gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, gmx_bool bFirst);

/** Sets the number of positions in a position structure. */
void
gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
/** Sets the evaluation group of a position data structure. */
void
gmx_ana_pos_set_evalgrp(gmx_ana_pos_t *pos, gmx_ana_index_t *g);
/** Empties a position data structure with full initialization. */
void
gmx_ana_pos_empty_init(gmx_ana_pos_t *pos);
/** Empties a position data structure. */
void
gmx_ana_pos_empty(gmx_ana_pos_t *pos);
/** Appends a position to a preallocated data structure with full
 * initialization. */
void
gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
                        gmx_ana_pos_t *src, int i);
/** Appends a position to a preallocated data structure. */
void
gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
                   gmx_ana_pos_t *src, int i, int refid);
/** Updates position data structure state after appends. */
void
gmx_ana_pos_append_finish(gmx_ana_pos_t *pos);

#ifdef __cplusplus
}
#endif

#endif