--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/04/14 15:37:41	1108
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/05/01 18:52:38	1144
@@ -63,6 +63,7 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
+  useMolecularCutoffs = 0;
 
   excludes = Exclude::Instance();
 
@@ -70,6 +71,8 @@ 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]) {
@@ -322,10 +325,16 @@ int SimInfo::getNDF(){
 int SimInfo::getNDF(){
   int ndf_local;
 
+  ndf_local = 0;
+  
   for(int i = 0; i < integrableObjects.size(); i++){
     ndf_local += 3;
-    if (integrableObjects[i]->isDirectional())
-      ndf_local += 3;
+    if (integrableObjects[i]->isDirectional()) {
+      if (integrableObjects[i]->isLinear())
+        ndf_local += 2;
+      else
+        ndf_local += 3;
+    }
   }
 
   // n_constraints is local, so subtract them on each processor:
@@ -350,11 +359,16 @@ int SimInfo::getNDFraw() {
   int ndfRaw_local;
 
   // Raw degrees of freedom that we have to set
+  ndfRaw_local = 0;
 
   for(int i = 0; i < integrableObjects.size(); i++){
     ndfRaw_local += 3;
-    if (integrableObjects[i]->isDirectional())
-      ndfRaw_local += 3;
+    if (integrableObjects[i]->isDirectional()) {
+       if (integrableObjects[i]->isLinear())
+        ndfRaw_local += 2;
+      else
+        ndfRaw_local += 3;
+    }
   }
     
 #ifdef IS_MPI
@@ -428,7 +442,7 @@ void SimInfo::refreshSim(){
 
   n_exclude = excludes->getSize();
   excl = excludes->getFortranArray();
-
+  
 #ifdef IS_MPI
   n_global = mpiSim->getTotAtoms();
 #else
@@ -437,9 +451,11 @@ void SimInfo::refreshSim(){
 
   isError = 0;
 
+ getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
+
   setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
-		  &nGlobalExcludes, globalExcludes, molMembershipArray, 
-                  &isError );
+		                    &nGlobalExcludes, globalExcludes, molMembershipArray, 
+		                    &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError );
 
   if( isError ){
 
@@ -499,11 +515,11 @@ void SimInfo::checkCutOffs( void ){
                "\tCurrent Value of LJrcut = %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, %G"
+	       "\n"
 	       "\t[ %G %G %G ]\n"
 	       "\t[ %G %G %G ]\n"
 	       "\t[ %G %G %G ]\n",
-	       rCut, currentTime, maxCutoff,
+	       rCut, 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]);
@@ -578,13 +594,55 @@ GenericData* SimInfo::getProperty(const string& propNa
     return NULL;  
 }
 
-vector<GenericData*> SimInfo::getProperties(){
 
-  vector<GenericData*> result;
-  map<string, GenericData*>::iterator i;
-  
-  for(i = properties.begin(); i != properties.end(); i++)
-    result.push_back((*i).second);
+void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup, 
+                                                          vector<int>& groupList, vector<int>& groupStart){
+  Molecule* mol;
+  int numAtom;
+  int curIndex;
+
+  mfact.clear();
+  groupList.clear();
+  groupStart.clear();
+
+  //Be careful, fortran array begin at 1
+  curIndex = 1;
     
-  return result;
+  if(info->useMolecularCutoffs){
+    //if using molecular cutoff
+    ngroup = info->n_mol;
+
+    for(int i = 0; i < ngroup; i ++){
+      mol = &(info->molecules[i]);
+      numAtom = mol->getNAtoms();
+      
+      for(int j=0; j < numAtom; j++){
+#ifdef IS_MPI
+        groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
+#else
+        groupList.push_back((info->atoms[i])->getIndex() + 1);
+#endif
+      }//for(int j=0; j < numAtom; j++)
+            
+      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
+    ngroup = info->n_atoms;
+    for(int i =0 ; i < ngroup; i++){
+      groupStart.push_back(curIndex++); 
+
+#ifdef IS_MPI
+      groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
+#else
+      groupList.push_back((info->atoms[i])->getIndex() + 1);
+#endif
+
+    }//end for(int i =0 ; i < ngroup; i++)
+
+  }//end if (info->useMolecularCutoffs)
+
 }