/*
 *  Groups of atoms, and interesting operations on them
 */

/* This is a cheesy way to do this and should be replaced, but it will do
 * for now, to place a limit on numbers of atoms, bonds, and terms, and
 * to declare arrays for them. Later I'll try to think of some more clever
 * arrangement so that these arrays can grow dynamically, and not have some
 * fundamental limit on their size.
 */

#define MAX_NUM_ATOMS 3000
#define MAX_NUM_BONDS 5000
#define MAX_NUM_TERMS 10000

typedef struct
  {
    atom *atoms[MAX_NUM_ATOMS];
    bond *bonds[MAX_NUM_BONDS];
    term *terms[MAX_NUM_TERMS];
    int atom_count;
    int bond_count;
    int term_count;
  }
group;

extern void init_group (group * g);

extern void add_atom (group * g, atom * a);
extern void add_bond (group * g, bond * b);
extern void add_term (group * g, term * t);
extern atom *choose_atom (group * g, int index);
extern bond *choose_bond (group * g, int index);
extern term *choose_term (group * g, int index);

/* total group energy is the sum of atoms' kinetic energies and terms'
 * potential energies. dampers dissipate energy and do not contribute
 * to this sum.
 */
extern double energy (group * g);

/* iterate atom motions, zero atom forces, compute term forces for new
 * positions of atoms
 */
extern void physics_time_step (group * g, double dt);

/* apply a test to all the atoms in this group, those that test
 * true are added to the 'selected' group. 'selector' should return
 * a boolean.
 */
extern void select_subgroup (group * g, group * selected,
			     int (*selector) (atom * atm, int index));

extern void apply_to_atoms (group * g, int (*do_this) (atom * a));
extern void apply_to_terms (group * g, int (*do_this) (term * t));

/* this is a slow operation [O(n^2) in number of atoms] so don't
 * do this very often for large structures
 */
extern void infer_bonds_from_distances (group * g);