--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/07 21:35:05	1150
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/27 00:48:12	1198
@@ -42,11 +42,10 @@ SimInfo::SimInfo(){
   thermalTime = 0.0;
   currentTime = 0.0;
   rCut = 0.0;
-  ecr = 0.0;
-  est = 0.0;
+  rSw = 0.0;
 
   haveRcut = 0;
-  haveEcr = 0;
+  haveRsw = 0;
   boxIsInit = 0;
   
   resetTime = 1e99;
@@ -63,7 +62,9 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
-  useMolecularCutoffs = 0;
+  useThermInt = 0;
+
+  haveCutoffGroups = false;
 
   excludes = Exclude::Instance();
 
@@ -452,7 +453,9 @@ 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);
@@ -480,29 +483,18 @@ void SimInfo::setDefaultRcut( double theRcut ){
   
   haveRcut = 1;
   rCut = theRcut;
+  rList = rCut + 1.0; 
   
-  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
-  
-  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+  notifyFortranCutOffs( &rCut, &rSw, &rList );
 }
 
-void SimInfo::setDefaultEcr( double theEcr ){
+void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
 
-  haveEcr = 1;
-  ecr = theEcr;
-  
-  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
-
-  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+  rSw = theRsw;
+  setDefaultRcut( theRcut );
 }
 
-void SimInfo::setDefaultEcr( double theEcr, double theEst ){
 
-  est = theEst;
-  setDefaultEcr( theEcr );
-}
-
-
 void SimInfo::checkCutOffs( void ){
   
   if( boxIsInit ){
@@ -511,8 +503,8 @@ void SimInfo::checkCutOffs( void ){
     
     if( rCut > maxCutoff ){
       sprintf( painCave.errMsg,
-	       "LJrcut is too large for the current periodic box.\n"
-               "\tCurrent Value of LJrcut = %G at time %G\n "
+	       "cutoffRadius is too large for the current periodic box.\n"
+               "\tCurrent Value of cutoffRadius = %G at time %G\n "
                "\tThis is larger than half of at least one of the\n"
                "\tperiodic box vectors.  Right now, the Box matrix is:\n"
 	       "\n"
@@ -525,28 +517,7 @@ void SimInfo::checkCutOffs( void ){
 	       Hmat[2][0], Hmat[2][1], Hmat[2][2]);
       painCave.isFatal = 1;
       simError();
-    }
-    
-    if( haveEcr ){
-      if( ecr > maxCutoff ){
-	sprintf( painCave.errMsg,
-                 "electrostaticCutoffRadius is too large for the current\n"
-                 "\tperiodic box.\n\n"
-                 "\tCurrent Value of ECR = %G at time %G\n "
-                 "\tThis is larger than half of at least one of the\n"
-                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
-                 "\n"
-                 "\t[ %G %G %G ]\n"
-                 "\t[ %G %G %G ]\n"
-                 "\t[ %G %G %G ]\n",
-		 ecr, currentTime,
-		 Hmat[0][0], Hmat[0][1], Hmat[0][2],
-		 Hmat[1][0], Hmat[1][1], Hmat[1][2],
-		 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
-	painCave.isFatal = 1;
-	simError();
-      }
-    }
+    }    
   } else {
     // initialize this stuff before using it, OK?
     sprintf( painCave.errMsg,
@@ -597,65 +568,51 @@ 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();
       
+      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
+                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
+        mfact.push_back(cutoffAtom->getMass()/totalMass);
+        groupList.push_back(cutoffAtom->getIndex() + 1);
+      }  
+                              
       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();
-#else
-    ngroup = info->n_atoms;
-#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)
-  
+      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 
+  groupStart.push_back(curIndex);
+  ngroup = groupStart.size() - 1;
 }