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32 * \brief API for handling positions.
34 * \author Teemu Murtola <teemu.murtola@cbr.su.se>
35 * \ingroup module_selection
37 #ifndef GMX_SELECTION_POSITION_H
38 #define GMX_SELECTION_POSITION_H
40 #include "../legacyheaders/types/simple.h"
42 #include "indexutil.h"
45 * Stores a set of positions together with their origins.
47 typedef struct gmx_ana_pos_t
50 * Number of positions.
58 * Velocities (can be NULL).
62 * Forces (can be NULL).
66 * Mapping of the current positions to the original group.
68 * \see gmx_ana_indexmap_t
72 * Pointer to the current evaluation group.
76 * Number of elements allocated for \c x.
81 /** Initializes an empty position structure. */
83 gmx_ana_pos_clear(gmx_ana_pos_t *pos);
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 /** Initializes a \c gmx_ana_pos_t to represent a constant position. */
95 gmx_ana_pos_init_const(gmx_ana_pos_t *pos, rvec x);
96 /** Frees the memory allocated for position storage. */
98 gmx_ana_pos_deinit(gmx_ana_pos_t *pos);
99 /** Frees the memory allocated for positions. */
101 gmx_ana_pos_free(gmx_ana_pos_t *pos);
102 /** Copies the evaluated positions to a preallocated data structure. */
104 gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst);
106 /** Sets the number of positions in a position structure. */
108 gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
109 /** Sets the evaluation group of a position data structure. */
111 gmx_ana_pos_set_evalgrp(gmx_ana_pos_t *pos, gmx_ana_index_t *g);
112 /** Empties a position data structure with full initialization. */
114 gmx_ana_pos_empty_init(gmx_ana_pos_t *pos);
115 /** Empties a position data structure. */
117 gmx_ana_pos_empty(gmx_ana_pos_t *pos);
118 /** Appends a position to a preallocated data structure with full
121 gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
122 gmx_ana_pos_t *src, int i);
123 /** Appends a position to a preallocated data structure. */
125 gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
126 gmx_ana_pos_t *src, int i, int refid);
127 /** Updates position data structure state after appends. */
129 gmx_ana_pos_append_finish(gmx_ana_pos_t *pos);