--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/11 16:00:22	1154
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/06/01 17:15:43	1212
@@ -62,6 +62,10 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
+  useSolidThermInt = 0;
+  useLiquidThermInt = 0;
+
+  haveCutoffGroups = false;
 
   excludes = Exclude::Instance();
 
@@ -442,7 +446,7 @@ void SimInfo::refreshSim(){
   excl = excludes->getFortranArray();
   
 #ifdef IS_MPI
-  n_global = mpiSim->getTotAtoms();
+  n_global = mpiSim->getNAtomsGlobal();
 #else
   n_global = n_atoms;
 #endif
@@ -450,7 +454,9 @@ void SimInfo::refreshSim(){
   isError = 0;
   
   getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
-  
+  //it may not be a good idea to pass the address of first element in vector
+  //since c++ standard does not require vector to be stored continuously in meomory
+  //Most of the compilers will organize the memory of vector continuously
   setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
                   &nGlobalExcludes, globalExcludes, molMembershipArray, 
                   &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
@@ -563,65 +569,54 @@ void getFortranGroupArray(SimInfo* info, vector<double
 
 void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
                           vector<int>& groupList, vector<int>& groupStart){
-  Molecule* mol;
+  Molecule* myMols;
   Atom** myAtoms;
   int numAtom;
   int curIndex;
   double mtot;
-
+  int numMol;
+  int numCutoffGroups;
+  CutoffGroup* myCutoffGroup;
+  vector<CutoffGroup*>::iterator iterCutoff;
+  Atom* cutoffAtom;
+  vector<Atom*>::iterator iterAtom;
+  int atomIndex;
+  double totalMass;
+  
   mfact.clear();
   groupList.clear();
   groupStart.clear();
   
   //Be careful, fortran array begin at 1
   curIndex = 1;
-  
-  if(info->useMolecularCutoffs){
-    
-#ifdef IS_MPI
-    ngroup = mpiSim->getMyNMol();
-#else
-    ngroup = info->n_mol;
-#endif
-    
-    for(int i = 0; i < ngroup; i ++){
-      mol = &(info->molecules[i]);
-      numAtom = mol->getNAtoms();
-      myAtoms = mol->getMyAtoms();
-      mtot = 0.0;
-
-      for(int j=0; j < numAtom; j++)
-        mtot += myAtoms[j]->getMass();                
-      
-      for(int j=0; j < numAtom; j++){ 
-               
-        // We want the local Index:
-        groupList.push_back(myAtoms[j]->getIndex() + 1);
-        mfact.push_back(myAtoms[j]->getMass() / mtot);
+
+  myMols = info->molecules;
+  numMol = info->n_mol;
+  for(int i  = 0; i < numMol; i++){
+    numCutoffGroups = myMols[i].getNCutoffGroups();
+    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; 
+                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
 
-      }
+      totalMass = myCutoffGroup->getMass();
       
-      groupStart.push_back(curIndex);
-      curIndex += numAtom;
-      
-    } //end for(int i =0 ; i < ngroup; i++)    
-  }
-  else{
-    //using atomic cutoff, every single atom is just a group
-    
-#ifdef IS_MPI
-    ngroup = mpiSim->getMyNlocal();
+      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
+                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
+        mfact.push_back(cutoffAtom->getMass()/totalMass);
+#ifdef IS_MPI        
+        groupList.push_back(cutoffAtom->getGlobalIndex() + 1);
 #else
-    ngroup = info->n_atoms;
+        groupList.push_back(cutoffAtom->getIndex() + 1);
 #endif
-    
-    for(int i =0 ; i < ngroup; i++){
-      groupStart.push_back(curIndex++);       
-      groupList.push_back((info->atoms[i])->getIndex() + 1);
-      mfact.push_back(1.0);
-      
-    }//end for(int i =0 ; i < ngroup; i++)
-    
-  }//end if (info->useMolecularCutoffs)
-  
+      }  
+                              
+      groupStart.push_back(curIndex);
+      curIndex += myCutoffGroup->getNumAtom();
+
+    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
+
+  }//end for(int i  = 0; i < numMol; i++)
+
+
+  //The last cutoff group need more element to indicate the end of the cutoff 
+  ngroup = groupStart.size();
 }