--- branches/development/src/parallel/ForceMatrixDecomposition.cpp	2011/08/12 19:59:56	1612
+++ branches/development/src/parallel/ForceMatrixDecomposition.cpp	2011/08/18 20:18:19	1613
@@ -233,26 +233,7 @@ namespace OpenMD {
       }      
     }
 
-#endif
-
-    // allocate memory for the parallel objects
-    atypesLocal.resize(nLocal_);
-
-    for (int i = 0; i < nLocal_; i++) 
-      atypesLocal[i] = ff_->getAtomType(idents[i]);
-
-    groupList_.clear();
-    groupList_.resize(nGroups_);
-    for (int i = 0; i < nGroups_; i++) {
-      int gid = cgLocalToGlobal[i];
-      for (int j = 0; j < nLocal_; j++) {
-        int aid = AtomLocalToGlobal[j];
-        if (globalGroupMembership[aid] == gid) {
-          groupList_[i].push_back(j);
-        }
-      }      
-    }
-
+#else
     excludesForAtom.clear();
     excludesForAtom.resize(nLocal_);
     toposForAtom.clear();
@@ -266,9 +247,10 @@ namespace OpenMD {
       for (int j = 0; j < nLocal_; j++) {
         int jglob = AtomLocalToGlobal[j];
 
-        if (excludes->hasPair(iglob, jglob)) 
+        if (excludes->hasPair(iglob, jglob))           
           excludesForAtom[i].push_back(j);              
         
+        
         if (oneTwo->hasPair(iglob, jglob)) {
           toposForAtom[i].push_back(j);
           topoDist[i].push_back(1);
@@ -285,7 +267,27 @@ namespace OpenMD {
         }
       }      
     }
-    
+#endif
+
+    // allocate memory for the parallel objects
+    atypesLocal.resize(nLocal_);
+
+    for (int i = 0; i < nLocal_; i++) 
+      atypesLocal[i] = ff_->getAtomType(idents[i]);
+
+    groupList_.clear();
+    groupList_.resize(nGroups_);
+    for (int i = 0; i < nGroups_; i++) {
+      int gid = cgLocalToGlobal[i];
+      for (int j = 0; j < nLocal_; j++) {
+        int aid = AtomLocalToGlobal[j];
+        if (globalGroupMembership[aid] == gid) {
+          groupList_[i].push_back(j);
+        }
+      }      
+    }
+
+
     createGtypeCutoffMap();
 
   }
@@ -683,8 +685,9 @@ namespace OpenMD {
       }
       
       AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
-      for (int i = 0; i < ns; i++)
+      for (int i = 0; i < ns; i++) 
         snap_->atomData.skippedCharge[i] += skch_tmp[i];
+            
     }
     
     nLocal_ = snap_->getNumberOfAtoms();
@@ -714,6 +717,13 @@ namespace OpenMD {
       pairwisePot[ii] = ploc2;
     }
 
+    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
+      RealType ploc1 = embeddingPot[ii];
+      RealType ploc2 = 0.0;
+      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
+      embeddingPot[ii] = ploc2;
+    }
+
 #endif
 
   }
@@ -855,18 +865,13 @@ namespace OpenMD {
    * field) must still be handled for these pairs.
    */
   bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
-    int unique_id_2;
-#ifdef IS_MPI
-    // in MPI, we have to look up the unique IDs for the row atom.
-    unique_id_2 = AtomColToGlobal[atom2];
-#else
-    // in the normal loop, the atom numbers are unique
-    unique_id_2 = atom2;
-#endif
+
+    // excludesForAtom was constructed to use row/column indices in the MPI
+    // version, and to use local IDs in the non-MPI version:
     
     for (vector<int>::iterator i = excludesForAtom[atom1].begin();
          i != excludesForAtom[atom1].end(); ++i) {
-      if ( (*i) == unique_id_2 ) return true;
+      if ( (*i) == atom2 )  return true;
     }
 
     return false;