include/position.h

   1 /*
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   3  *                This source code is part of
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  31 /*! \file
  32  * \brief API for handling positions.
  33  */
  34 #ifndef POSITION_H
  35 #define POSITION_H
  36
  37 #include <typedefs.h>
  38
  39 #include <indexutil.h>
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45 /*! \brief
  46  * Stores a set of positions together with their origins.
  47  */
  48 typedef struct gmx_ana_pos_t
  49 {
  50     /*! \brief
  51      * Number of positions.
  52      */
  53     int                 nr;
  54     /*! \brief
  55      * Array of positions.
  56      */
  57     rvec               *x;
  58     /*! \brief
  59      * Velocities (can be NULL).
  60      */
  61     rvec               *v;
  62     /*! \brief
  63      * Forces (can be NULL).
  64      */
  65     rvec               *f;
  66     /*! \brief
  67      * Mapping of the current positions to the original group.
  68      *
  69      * \see gmx_ana_indexmap_t
  70      */
  71     gmx_ana_indexmap_t  m;
  72     /*! \brief
  73      * Pointer to the current evaluation group.
  74      */
  75     gmx_ana_index_t    *g;
  76     /*! \brief
  77      * Number of elements allocated for \c x.
  78      */
  79     int                 nalloc_x;
  80 } gmx_ana_pos_t;
  81
  82 /** Initializes an empty position structure. */
  83 extern void
  84 gmx_ana_pos_clear(gmx_ana_pos_t *pos);
  85 /** Ensures that enough memory has been allocated to store positions. */
  86 extern void
  87 gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize);
  88 /** Request memory allocation for velocities. */
  89 extern void
  90 gmx_ana_pos_reserve_velocities(gmx_ana_pos_t *pos);
  91 /** Request memory allocation for forces. */
  92 extern void
  93 gmx_ana_pos_reserve_forces(gmx_ana_pos_t *pos);
  94 /** Initializes a \c gmx_ana_pos_t to represent a constant position. */
  95 extern void
  96 gmx_ana_pos_init_const(gmx_ana_pos_t *pos, rvec x);
  97 /** Frees the memory allocated for position storage. */
  98 extern void
  99 gmx_ana_pos_deinit(gmx_ana_pos_t *pos);
 100 /** Frees the memory allocated for positions. */
 101 extern void
 102 gmx_ana_pos_free(gmx_ana_pos_t *pos);
 103 /** Copies the evaluated positions to a preallocated data structure. */
 104 extern void
 105 gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst);
 106
 107 /** Sets the number of positions in a position structure. */
 108 extern void
 109 gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
 110 /** Sets the evaluation group of a position data structure. */
 111 extern void
 112 gmx_ana_pos_set_evalgrp(gmx_ana_pos_t *pos, gmx_ana_index_t *g);
 113 /** Empties a position data structure with full initialization. */
 114 extern void
 115 gmx_ana_pos_empty_init(gmx_ana_pos_t *pos);
 116 /** Empties a position data structure. */
 117 extern void
 118 gmx_ana_pos_empty(gmx_ana_pos_t *pos);
 119 /** Appends a position to a preallocated data structure with full
 120  * initialization. */
 121 extern void
 122 gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
 123                         gmx_ana_pos_t *src, int i);
 124 /** Appends a position to a preallocated data structure. */
 125 extern void
 126 gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
 127                    gmx_ana_pos_t *src, int i, int refid);
 128 /** Updates position data structure state after appends. */
 129 extern void
 130 gmx_ana_pos_append_finish(gmx_ana_pos_t *pos);
 131
 132 #ifdef __cplusplus
 133 }
 134 #endif
 135
 136 #endif