--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/04/22 21:33:55	1131
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/07 21:35:05	1150
@@ -63,6 +63,7 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
+  useMolecularCutoffs = 0;
 
   excludes = Exclude::Instance();
 
@@ -71,6 +72,8 @@ SimInfo::SimInfo(){
   has_minimizer = false;
   the_minimizer =NULL;
 
+  ngroup = 0;
+
   wrapMeSimInfo( this );
 }
 
@@ -83,7 +86,7 @@ SimInfo::~SimInfo(){
   
   for(i = properties.begin(); i != properties.end(); i++)
     delete (*i).second;
-    
+  
 }
 
 void SimInfo::setBox(double newBox[3]) {
@@ -439,45 +442,47 @@ void SimInfo::refreshSim(){
 
   n_exclude = excludes->getSize();
   excl = excludes->getFortranArray();
-
+  
 #ifdef IS_MPI
   n_global = mpiSim->getTotAtoms();
 #else
   n_global = n_atoms;
 #endif
-
+  
   isError = 0;
-
-  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
-		  &nGlobalExcludes, globalExcludes, molMembershipArray, 
-                  &isError );
-
+  
+  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
+  
+  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
+                  &nGlobalExcludes, globalExcludes, molMembershipArray, 
+                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
+  
   if( isError ){
-
+    
     sprintf( painCave.errMsg,
-	     "There was an error setting the simulation information in fortran.\n" );
+             "There was an error setting the simulation information in fortran.\n" );
     painCave.isFatal = 1;
     simError();
   }
-
+  
 #ifdef IS_MPI
   sprintf( checkPointMsg,
 	   "succesfully sent the simulation information to fortran.\n");
   MPIcheckPoint();
 #endif // is_mpi
-
+  
   this->ndf = this->getNDF();
   this->ndfRaw = this->getNDFraw();
   this->ndfTrans = this->getNDFtranslational();
 }
 
 void SimInfo::setDefaultRcut( double theRcut ){
-
+  
   haveRcut = 1;
   rCut = theRcut;
-
+  
   ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
-
+  
   notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
 }
 
@@ -588,4 +593,69 @@ GenericData* SimInfo::getProperty(const string& propNa
   else   
     return NULL;  
 }
+
+
+void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
+                          vector<int>& groupList, vector<int>& groupStart){
+  Molecule* mol;
+  Atom** myAtoms;
+  int numAtom;
+  int curIndex;
+  double mtot;
+
+  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);
+
+      }
+      
+      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)
+  
+}