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36 * \brief API for handling positions.
38 * \author Teemu Murtola <teemu.murtola@gmail.com>
39 * \ingroup module_selection
41 #ifndef GMX_SELECTION_POSITION_H
42 #define GMX_SELECTION_POSITION_H
44 #include "../legacyheaders/types/simple.h"
46 #include "indexutil.h"
49 * Stores a set of positions together with their origins.
53 //! Initializes an empty position structure.
57 //! Returns the number of positions.
58 int count() const { return m.mapb.nr; }
65 * Velocities (can be NULL).
69 * Forces (can be NULL).
73 * Mapping of the current positions to the original group.
75 * \see gmx_ana_indexmap_t
79 * Number of elements allocated for \c x.
84 /** Ensures that enough memory has been allocated to store positions. */
86 gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize);
87 /** Request memory allocation for velocities. */
89 gmx_ana_pos_reserve_velocities(gmx_ana_pos_t *pos);
90 /** Request memory allocation for forces. */
92 gmx_ana_pos_reserve_forces(gmx_ana_pos_t *pos);
93 /** Reserves memory for use with gmx_ana_pos_append_init(). */
95 gmx_ana_pos_reserve_for_append(gmx_ana_pos_t *pos, int n, int isize,
96 bool bVelocities, bool bForces);
97 /** Initializes a \c gmx_ana_pos_t to represent a constant position. */
99 gmx_ana_pos_init_const(gmx_ana_pos_t *pos, const rvec x);
100 /** Copies the evaluated positions to a preallocated data structure. */
102 gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst);
104 /** Sets the number of positions in a position structure. */
106 gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
107 /** Empties a position data structure with full initialization. */
109 gmx_ana_pos_empty_init(gmx_ana_pos_t *pos);
110 /** Empties a position data structure. */
112 gmx_ana_pos_empty(gmx_ana_pos_t *pos);
113 /** Appends a position to a preallocated data structure with full
116 gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, int i);
117 /** Appends a position to a preallocated data structure. */
119 gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, int i, int refid);
120 /** Updates position data structure state after appends. */
122 gmx_ana_pos_append_finish(gmx_ana_pos_t *pos);
124 /** Appends atoms from a position into a preallocated index group. */
125 gmx_ana_pos_add_to_group(gmx_ana_index_t *g, gmx_ana_pos_t *src, int i);