libgromacs-dev 5.1.2-1ubuntu1 / usr / include / gromacs / topology / block.h

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#ifndef GMX_TOPOLOGY_BLOCK_H
#define GMX_TOPOLOGY_BLOCK_H

#include "gromacs/legacyheaders/types/simple.h"

#ifdef __cplusplus
extern "C" {
#endif

/* the block structure points into an array (usually of atom_ids).
   It is a list of starting indices for objects of consecutive ids, such
   as molecules.
   For example, if this block denotes molecules, then the first molecule
   ranges from index[0] to index[1]-1 in the atom list.

   This makes the mapping from atoms to molecules O(Nmolecules) instead
   of O(Natoms) in size.  */
typedef struct t_block
{
    int      nr;           /* The number of blocks          */
    atom_id *index;        /* Array of indices (dim: nr+1)  */
    int      nalloc_index; /* The allocation size for index */
} t_block;

typedef struct t_blocka
{
    int      nr;    /* The number of blocks              */
    atom_id *index; /* Array of indices in a (dim: nr+1) */
    int      nra;   /* The number of atoms               */
    atom_id *a;     /* Array of atom numbers in each group  */
    /* (dim: nra)                           */
    /* Block i (0<=i<nr) runs from          */
    /* index[i] to index[i+1]-1. There will */
    /* allways be an extra entry in index   */
    /* to terminate the table               */
    int nalloc_index;           /* The allocation size for index        */
    int nalloc_a;               /* The allocation size for a            */
} t_blocka;

void init_block(t_block *block);
void init_blocka(t_blocka *block);
t_blocka *new_blocka(void);
/* allocate new block */

void done_block(t_block *block);
void done_blocka(t_blocka *block);

void copy_blocka(const t_blocka *src, t_blocka *dest);

void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
/* Fill a block structure with numbers identical to the index
 * (0, 1, 2, .. natom-1)
 * If bOneIndexGroup, then all atoms are  lumped in one index group,
 * otherwise there is one atom per index entry
 */

void stupid_fill_blocka(t_blocka *grp, int natom);
/* Fill a block structure with numbers identical to the index
 * (0, 1, 2, .. natom-1)
 * There is one atom per index entry
 */

#ifdef __cplusplus
}
#endif

#endif