src/gromacs/topology/block.h

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  37 #ifndef GMX_TOPOLOGY_BLOCK_H
  38 #define GMX_TOPOLOGY_BLOCK_H
  39
  40 #include "gromacs/legacyheaders/types/simple.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46 /* the block structure points into an array (usually of atom_ids).
  47    It is a list of starting indices for objects of consecutive ids, such
  48    as molecules.
  49    For example, if this block denotes molecules, then the first molecule
  50    ranges from index[0] to index[1]-1 in the atom list.
  51
  52    This makes the mapping from atoms to molecules O(Nmolecules) instead
  53    of O(Natoms) in size.  */
  54 typedef struct t_block
  55 {
  56     int      nr;           /* The number of blocks          */
  57     atom_id *index;        /* Array of indices (dim: nr+1)  */
  58     int      nalloc_index; /* The allocation size for index */
  59 } t_block;
  60
  61 typedef struct t_blocka
  62 {
  63     int      nr;    /* The number of blocks              */
  64     atom_id *index; /* Array of indices in a (dim: nr+1) */
  65     int      nra;   /* The number of atoms               */
  66     atom_id *a;     /* Array of atom numbers in each group  */
  67     /* (dim: nra)                           */
  68     /* Block i (0<=i<nr) runs from          */
  69     /* index[i] to index[i+1]-1. There will */
  70     /* allways be an extra entry in index   */
  71     /* to terminate the table               */
  72     int nalloc_index;           /* The allocation size for index        */
  73     int nalloc_a;               /* The allocation size for a            */
  74 } t_blocka;
  75
  76 void init_block(t_block *block);
  77 void init_blocka(t_blocka *block);
  78 t_blocka *new_blocka(void);
  79 /* allocate new block */
  80
  81 void done_block(t_block *block);
  82 void done_blocka(t_blocka *block);
  83
  84 void copy_blocka(const t_blocka *src, t_blocka *dest);
  85
  86 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
  87 /* Fill a block structure with numbers identical to the index
  88  * (0, 1, 2, .. natom-1)
  89  * If bOneIndexGroup, then all atoms are  lumped in one index group,
  90  * otherwise there is one atom per index entry
  91  */
  92
  93 void stupid_fill_blocka(t_blocka *grp, int natom);
  94 /* Fill a block structure with numbers identical to the index
  95  * (0, 1, 2, .. natom-1)
  96  * There is one atom per index entry
  97  */
  98
  99 #ifdef __cplusplus
 100 }
 101 #endif
 102
 103 #endif