--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/06/01 17:15:43	1212
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/06/01 18:42:58	1214
@@ -171,8 +171,8 @@ void SimSetup::makeMolecules(void){
   int i, j, k;
   int exI, exJ, exK, exL, slI, slJ;
   int tempI, tempJ, tempK, tempL;
-  int molI;
-  int stampID, atomOffset, rbOffset;
+  int molI, globalID;
+  int stampID, atomOffset, rbOffset, groupOffset;
   molInit molInfo;
   DirectionalAtom* dAtom;
   RigidBody* myRB;
@@ -216,6 +216,16 @@ void SimSetup::makeMolecules(void){
   for (k = 0; k < nInfo; k++){
     the_ff->setSimInfo(&(info[k]));
 
+#ifdef IS_MPI
+    info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
+    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) 
+      info[k].globalGroupMembership[i] = 0;
+#else
+    info[k].globalGroupMembership = new int[info[k].n_atoms];
+    for (i = 0; i < info[k].n_atoms; i++) 
+      info[k].globalGroupMembership[i] = 0;
+#endif
+
     atomOffset = 0;
     groupOffset = 0;
 
@@ -282,9 +292,7 @@ void SimSetup::makeMolecules(void){
 
         molInfo.myAtoms[j]->setType(currentAtom->getType());
 #ifdef IS_MPI
-
         molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
-
 #endif // is_mpi
       } 
 
@@ -506,7 +514,12 @@ void SimSetup::makeMolecules(void){
         nMembers = currentCutoffGroup->getNMembers(); 
 
         myCutoffGroup = new CutoffGroup();
+        
+#ifdef IS_MPI
         myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
+#else
+        myCutoffGroup->setGlobalIndex(j + groupOffset);
+#endif
         
         for (int cg = 0; cg < nMembers; cg++) {
 
@@ -517,37 +530,42 @@ void SimSetup::makeMolecules(void){
           tempI = molI + atomOffset;
 
 #ifdef IS_MPI
-          globalID = info[k].atoms[tempI]->getGlobalIndex()
+          globalID = info[k].atoms[tempI]->getGlobalIndex();
+          info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
 #else 
           globalID = info[k].atoms[tempI]->getIndex();
+          info[k].globalGroupMembership[globalID] = j + groupOffset;
 #endif
+          
 
-          globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; 
-
+          
           myCutoffGroup->addAtom(info[k].atoms[tempI]);          
-
+          
           cutoffAtomSet.insert(tempI);
         }
-       
+        
         molInfo.myCutoffGroups.push_back(myCutoffGroup);
         groupOffset++;
 
       }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
-
+      
       //creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
-
+      
       for(j = 0; j < molInfo.nAtoms; j++){
-
+        
         if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
           myCutoffGroup = new CutoffGroup();
           myCutoffGroup->addAtom(molInfo.myAtoms[j]);
-          myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
-#ifdef IS_MPI
-          globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
-#else 
+
+#ifdef IS_MPI
+          myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
+          globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
+          info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; 
+#else
+          myCutoffGroup->setGlobalIndex(j + groupOffset);
           globalID = info[k].atoms[atomOffset + j]->getIndex();
+          info[k].globalGroupMembership[globalID] = j+groupOffset;
 #endif
-          globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; 
           molInfo.myCutoffGroups.push_back(myCutoffGroup);
           groupOffset++;
         }
@@ -641,13 +659,39 @@ void SimSetup::makeMolecules(void){
                                  theTorsions);
 
       info[k].molecules[i].initialize(molInfo);
-
-
+      
+      
       atomOffset += molInfo.nAtoms;
       delete[] theBonds;
       delete[] theBends;
       delete[] theTorsions;
-    }    
+    }
+
+
+
+#ifdef IS_MPI    
+    // Since the globalGroupMembership has been zero filled and we've only
+    // poked values into the atoms we know, we can do an Allreduce
+    // to get the full globalGroupMembership array (We think).
+    // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
+    // docs said we could.
+
+    int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];    
+
+    MPI_Allreduce(info[k].globalGroupMembership,
+                  ggMjunk,
+                  mpiSim->getNAtomsGlobal(),
+                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+
+    for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) 
+      info[k].globalGroupMembership[i] = ggMjunk[i];
+
+    delete[] ggMjunk;
+    
+#endif
+
+
+
   }
 
 #ifdef IS_MPI
@@ -1609,6 +1653,7 @@ void SimSetup::mpiMolDivide(void){
 
   mpiSim->divideLabor();
   globalAtomIndex = mpiSim->getGlobalAtomIndex();
+  globalGroupIndex = mpiSim->getGlobalGroupIndex();
   //globalMolIndex = mpiSim->getGlobalMolIndex();
 
   // set up the local variables