Merge pull request #953 from jrgissing/bond/react-update

 private:

  int me,nprocs;

  int newton_bond;

  int nreacts;

  int *nevery;

  FILE *fp;

  int maxcreate;

  int allncreate;

  tagint ***created;

  int *local_ncreate;

  class Molecule *onemol; // pre-reacted molecule template

  class Molecule *twomol; // post-reacted molecule template

  int ***reverse_equiv; // re-ordered equivalences

  int **landlocked_atoms; // all atoms at least three bonds away from edge atoms

  int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors

  tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list

  int pion,neigh,trace; // important indices for various loops. required for restore points

  int lcl_inst; // reaction instance

  tagint **glove; // 1st colmn: pre-reacted template, 2nd colmn: global IDs

  void far_partner();

  void close_partner();

  void get_molxspecials();

  void find_landlocked_atoms(int);

  void glove_ghostcheck();

  void ghost_glovecast();

  void limit_bond(int);

  void dedup_mega_gloves(int); //dedup global mega_glove

  // DEBUG (currently obsolete)

  // DEBUG

  void print_bb();