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/*! \file
* \brief API for handling positions.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_POSITION_H
#define GMX_SELECTION_POSITION_H
#include "gromacs/math/vectypes.h"
#include "gromacs/selection/indexutil.h"
/*! \brief
* Stores a set of positions together with their origins.
*/
struct gmx_ana_pos_t
{
//! Initializes an empty position structure.
gmx_ana_pos_t();
~gmx_ana_pos_t();
//! Returns the number of positions.
int count() const { return m.mapb.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
* Number of elements allocated for \c x.
*/
int nalloc_x;
};
/** 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);
/** Reserves memory for use with gmx_ana_pos_append_init(). */
void
gmx_ana_pos_reserve_for_append(gmx_ana_pos_t *pos, int n, int isize,
bool bVelocities, bool bForces);
/** Initializes a \c gmx_ana_pos_t to represent a constant position. */
void
gmx_ana_pos_init_const(gmx_ana_pos_t *pos, const rvec x);
/** Copies the evaluated positions to a preallocated data structure. */
void
gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst);
/** Sets the number of positions in a position structure. */
void
gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
/** 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_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_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);
void
/** Appends atoms from a position into a preallocated index group. */
gmx_ana_pos_add_to_group(gmx_ana_index_t *g, gmx_ana_pos_t *src, int i);
#endif
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