src/gromacs/topology/block.h

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  37 #ifndef GMX_TOPOLOGY_BLOCK_H
  38 #define GMX_TOPOLOGY_BLOCK_H
  39
  40 #include <stdio.h>
  41
  42 #ifdef __cplusplus
  43 #include <vector>
  44 #endif
  45
  46 #include "gromacs/utility/basedefinitions.h"
  47 #ifdef __cplusplus
  48 #include "gromacs/utility/gmxassert.h"
  49 #endif
  50
  51 #ifdef __cplusplus
  52 extern "C" {
  53 #endif
  54
  55 #ifdef __cplusplus
  56 namespace gmx
  57 {
  58
  59 /*! \brief Division of a range of indices into consecutive blocks
  60  *
  61  * A range of consecutive indices 0 to index[numBlocks()] is divided
  62  * into numBlocks() consecutive blocks of consecutive indices.
  63  * Block b contains indices i for which index[b] <= i < index[b+1].
  64  */
  65 struct BlockRanges
  66 {
  67     /*! \brief Returns the number of blocks
  68      *
  69      * This should only be called on a valid struct. Validy is asserted
  70      * (only) in debug mode.
  71      */
  72     int numBlocks() const
  73     {
  74         GMX_ASSERT(index.size() > 0, "numBlocks() should only be called on a valid BlockRanges struct");
  75         return index.size() - 1;
  76     }
  77
  78     std::vector<int> index; /**< The list of block begin/end indices */
  79 };
  80
  81 }      // nsamespace gmx
  82 #endif // __cplusplus
  83
  84 /* Deprecated, C-style version of BlockRanges */
  85 typedef struct t_block
  86 {
  87     int      nr;           /* The number of blocks          */
  88     int     *index;        /* Array of indices (dim: nr+1)  */
  89     int      nalloc_index; /* The allocation size for index */
  90 } t_block;
  91
  92 typedef struct t_blocka
  93 {
  94     int      nr;    /* The number of blocks              */
  95     int     *index; /* Array of indices in a (dim: nr+1) */
  96     int      nra;   /* The number of atoms               */
  97     int     *a;     /* Array of atom numbers in each group  */
  98     /* (dim: nra)                           */
  99     /* Block i (0<=i<nr) runs from          */
 100     /* index[i] to index[i+1]-1. There will */
 101     /* allways be an extra entry in index   */
 102     /* to terminate the table               */
 103     int nalloc_index;           /* The allocation size for index        */
 104     int nalloc_a;               /* The allocation size for a            */
 105 } t_blocka;
 106
 107 void init_block(t_block *block);
 108 void init_blocka(t_blocka *block);
 109 t_blocka *new_blocka(void);
 110 /* allocate new block */
 111
 112 void done_block(t_block *block);
 113 void done_blocka(t_blocka *block);
 114
 115 void copy_blocka(const t_blocka *src, t_blocka *dest);
 116
 117 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
 118 /* Fill a block structure with numbers identical to the index
 119  * (0, 1, 2, .. natom-1)
 120  * If bOneIndexGroup, then all atoms are  lumped in one index group,
 121  * otherwise there is one atom per index entry
 122  */
 123
 124 void stupid_fill_blocka(t_blocka *grp, int natom);
 125 /* Fill a block structure with numbers identical to the index
 126  * (0, 1, 2, .. natom-1)
 127  * There is one atom per index entry
 128  */
 129
 130 void pr_block(FILE *fp, int indent, const char *title, const t_block *block, gmx_bool bShowNumbers);
 131 void pr_blocka(FILE *fp, int indent, const char *title, const t_blocka *block, gmx_bool bShowNumbers);
 132
 133 #ifdef __cplusplus
 134 }
 135 #endif
 136
 137 #endif