use list of bonds per atom instead of bondlist, as that will work with shake as well

    vector_atom = fragmentID;

  }

  int nbondlist = neighbor->nbondlist;

  int **bondlist = neighbor->bondlist;

  // if group is dynamic, insure ghost atom masks are current

  if (group->dynamic[igroup]) {

    comm->forward_comm_compute(this);

  }

  // every bond starts in its own fragment,

  // with fragmentID = MIN(b1atomID,b2atomID)

  // only bonds wholly contained in the group are considered

  // each atom starts in its own fragment,

  int nlocal = atom->nlocal;

  tagint *tag = atom->tag;

  int *mask = atom->mask;

  int *num_bond = atom->num_bond;

  tagint **bond_atom = atom->bond_atom;

  for (i = 0; i < nbondlist; i++) {

    const int b1 = bondlist[i][0];

    const int b2 = bondlist[i][1];

    if ((mask[b1] & groupbit) && (mask[b2] & groupbit))

      fragmentID[b1] = fragmentID[b2] = MIN(tag[b1],tag[b2]);

    else fragmentID[b1] = fragmentID[b2] = 0;

  }

  for (i = 0; i < nlocal + atom->nghost; i++)

    if (mask[i] & groupbit) fragmentID[i] = tag[i];

    else fragmentID[i] = 0;

  // loop until no more changes on any proc:

  // acquire fragmentIDs of ghost atoms

  // then check if any proc made changes

  commflag = 1;

  int nlocal = atom->nlocal;

  int *num_bond = atom->num_bond;

  tagint **bond_atom = atom->bond_atom;

  int change,done,anychange;

        if (!(mask[i] & groupbit)) continue;

        for (j = 0; j < num_bond[i]; j++) {

          k = bond_atom[i][j];

          k = atom->map(bond_atom[i][j]);

          if (k < 0) continue;

          if (!(mask[k] & groupbit)) continue;

          if (fragmentID[i] == fragmentID[k]) continue;