--- trunk/OOPSE/libmdtools/SimInfo.cpp	2004/04/14 15:37:41	1108
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2004/04/28 22:06:29	1139
@@ -63,6 +63,7 @@ SimInfo::SimInfo(){
   useReactionField = 0;
   useGB = 0;
   useEAM = 0;
+  useMolecularCutoffs = 0;
 
   excludes = Exclude::Instance();
 
@@ -322,10 +323,16 @@ 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 +357,16 @@ 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
@@ -425,6 +437,7 @@ void SimInfo::refreshSim(){
   //fInfo.SIM_uses_RF = 0;
   fInfo.SIM_uses_GB = useGB;
   fInfo.SIM_uses_EAM = useEAM;
+  fInfo.SIM_uses_molecular_cutoffs = useMolecularCutoffs;
 
   n_exclude = excludes->getSize();
   excl = excludes->getFortranArray();
@@ -499,11 +512,11 @@ 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 +591,3 @@ 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);
-    
-  return result;
-}