include/position.h

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  38 /*! \file
  39  * \brief API for handling positions.
  40  */
  41 #ifndef POSITION_H
  42 #define POSITION_H
  43
  44 #include "typedefs.h"
  45
  46 #include "indexutil.h"
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 /*! \brief
  53  * Stores a set of positions together with their origins.
  54  */
  55 typedef struct gmx_ana_pos_t
  56 {
  57     /*! \brief
  58      * Number of positions.
  59      */
  60     int                 nr;
  61     /*! \brief
  62      * Array of positions.
  63      */
  64     rvec               *x;
  65     /*! \brief
  66      * Velocities (can be NULL).
  67      */
  68     rvec               *v;
  69     /*! \brief
  70      * Forces (can be NULL).
  71      */
  72     rvec               *f;
  73     /*! \brief
  74      * Mapping of the current positions to the original group.
  75      *
  76      * \see gmx_ana_indexmap_t
  77      */
  78     gmx_ana_indexmap_t  m;
  79     /*! \brief
  80      * Pointer to the current evaluation group.
  81      */
  82     gmx_ana_index_t    *g;
  83     /*! \brief
  84      * Number of elements allocated for \c x.
  85      */
  86     int                 nalloc_x;
  87 } gmx_ana_pos_t;
  88
  89 /** Initializes an empty position structure. */
  90 void
  91 gmx_ana_pos_clear(gmx_ana_pos_t *pos);
  92 /** Ensures that enough memory has been allocated to store positions. */
  93 void
  94 gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize);
  95 /** Request memory allocation for velocities. */
  96 void
  97 gmx_ana_pos_reserve_velocities(gmx_ana_pos_t *pos);
  98 /** Request memory allocation for forces. */
  99 void
 100 gmx_ana_pos_reserve_forces(gmx_ana_pos_t *pos);
 101 /** Initializes a \c gmx_ana_pos_t to represent a constant position. */
 102 void
 103 gmx_ana_pos_init_const(gmx_ana_pos_t *pos, rvec x);
 104 /** Frees the memory allocated for position storage. */
 105 void
 106 gmx_ana_pos_deinit(gmx_ana_pos_t *pos);
 107 /** Frees the memory allocated for positions. */
 108 void
 109 gmx_ana_pos_free(gmx_ana_pos_t *pos);
 110 /** Copies the evaluated positions to a preallocated data structure. */
 111 void
 112 gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, gmx_bool bFirst);
 113
 114 /** Sets the number of positions in a position structure. */
 115 void
 116 gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
 117 /** Sets the evaluation group of a position data structure. */
 118 void
 119 gmx_ana_pos_set_evalgrp(gmx_ana_pos_t *pos, gmx_ana_index_t *g);
 120 /** Empties a position data structure with full initialization. */
 121 void
 122 gmx_ana_pos_empty_init(gmx_ana_pos_t *pos);
 123 /** Empties a position data structure. */
 124 void
 125 gmx_ana_pos_empty(gmx_ana_pos_t *pos);
 126 /** Appends a position to a preallocated data structure with full
 127  * initialization. */
 128 void
 129 gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
 130                         gmx_ana_pos_t *src, int i);
 131 /** Appends a position to a preallocated data structure. */
 132 void
 133 gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
 134                    gmx_ana_pos_t *src, int i, int refid);
 135 /** Updates position data structure state after appends. */
 136 void
 137 gmx_ana_pos_append_finish(gmx_ana_pos_t *pos);
 138
 139 #ifdef __cplusplus
 140 }
 141 #endif
 142
 143 #endif