diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp
index 02a0b8e7d..5024ada4f 100644
--- a/src/compute_fragment_atom.cpp
+++ b/src/compute_fragment_atom.cpp
@@ -1,210 +1,201 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
    certain rights in this software.  This software is distributed under
    the GNU General Public License.
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
    Contributing author: Axel Kohlmeyer (Temple U)
 ------------------------------------------------------------------------- */
 
 #include <string.h>
 #include "compute_fragment_atom.h"
 #include "atom.h"
 #include "atom_vec.h"
 #include "update.h"
 #include "modify.h"
 #include "neighbor.h"
 #include "force.h"
 #include "pair.h"
 #include "comm.h"
 #include "memory.h"
 #include "error.h"
 
 #include "group.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeFragmentAtom::ComputeFragmentAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
   fragmentID(NULL)
 {
   if (narg != 3) error->all(FLERR,"Illegal compute fragment/atom command");
 
   if (atom->avec->bonds_allow == 0)
     error->all(FLERR,"Compute fragment/atom used when bonds are not allowed");
 
   peratom_flag = 1;
   size_peratom_cols = 0;
   comm_forward = 1;
 
   nmax = 0;
 }
 
 /* ---------------------------------------------------------------------- */
 
 ComputeFragmentAtom::~ComputeFragmentAtom()
 {
   memory->destroy(fragmentID);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void ComputeFragmentAtom::init()
 {
   if (atom->tag_enable == 0)
     error->all(FLERR,"Cannot use compute fragment/atom unless atoms have IDs");
   if (force->bond == NULL)
     error->all(FLERR,"Compute fragment/atom requires a bond style to be defined");
 
   int count = 0;
   for (int i = 0; i < modify->ncompute; i++)
     if (strcmp(modify->compute[i]->style,"fragment/atom") == 0) count++;
   if (count > 1 && comm->me == 0)
     error->warning(FLERR,"More than one compute fragment/atom");
 }
 
 /* ---------------------------------------------------------------------- */
 
 void ComputeFragmentAtom::compute_peratom()
 {
   int i,j,k;
 
   invoked_peratom = update->ntimestep;
 
   // grow fragmentID array if necessary
 
   if (atom->nmax > nmax) {
     memory->destroy(fragmentID);
     nmax = atom->nmax;
     memory->create(fragmentID,nmax,"fragment/atom:fragmentID");
     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]) {
     commflag = 0;
     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
   // loop over my atoms, and check atoms bound to it
   // if both atoms are in fragment, assign lowest fragmentID to both
   // iterate until no changes in my 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;
 
   while (1) {
     comm->forward_comm_compute(this);
 
     change = 0;
     while (1) {
       done = 1;
       for (i = 0; i < nlocal; i++) {
         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;
 
           fragmentID[i] = fragmentID[k] = MIN(fragmentID[i],fragmentID[k]);
           done = 0;
         }
       }
       if (!done) change = 1;
       if (done) break;
     }
 
     // stop if all procs are done
 
     MPI_Allreduce(&change,&anychange,1,MPI_INT,MPI_MAX,world);
     if (!anychange) break;
   }
 }
 
 /* ---------------------------------------------------------------------- */
 
 int ComputeFragmentAtom::pack_forward_comm(int n, int *list, double *buf,
                                           int pbc_flag, int *pbc)
 {
   int i,j,m;
 
   m = 0;
   if (commflag) {
     for (i = 0; i < n; i++) {
       j = list[i];
       buf[m++] = fragmentID[j];
     }
   } else {
     int *mask = atom->mask;
     for (i = 0; i < n; i++) {
       j = list[i];
       buf[m++] = ubuf(mask[j]).d;
     }
   }
 
   return m;
 }
 
 /* ---------------------------------------------------------------------- */
 
 void ComputeFragmentAtom::unpack_forward_comm(int n, int first, double *buf)
 {
   int i,m,last;
 
   m = 0;
   last = first + n;
   if (commflag)
     for (i = first; i < last; i++) fragmentID[i] = buf[m++];
   else {
     int *mask = atom->mask;
     for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
   }
 }
 
 /* ----------------------------------------------------------------------
    memory usage of local atom-based array
 ------------------------------------------------------------------------- */
 
 double ComputeFragmentAtom::memory_usage()
 {
   double bytes = nmax * sizeof(double);
   return bytes;
 }