--- trunk/OOPSE/libmdtools/DUFF.cpp	2004/01/22 17:34:20	976
+++ trunk/OOPSE/libmdtools/DUFF.cpp	2004/04/12 20:32:20	1097
@@ -116,7 +116,7 @@ namespace DUFF_NS {  // restrict the access of the fol
     void printMe( void ){
       
       std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n";
-      if( next != NULL ) next->printMe();
+      //      if( next != NULL ) next->printMe();
 
     }
 
@@ -922,7 +922,7 @@ void DUFF::readParams( void ){
     fastForward( "BendTypes", "initializeBends" );
 
     // we are now at the bendTypes section
-
+    
     eof_test =  fgets( readLine, sizeof(readLine), frcFile );
     lineNum++;
         
@@ -1120,6 +1120,7 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
   // initialize the atoms
   
   DirectionalAtom* dAtom;
+  double ji[3];
 
   for(int i=0; i<nAtoms; i++ ){
 
@@ -1133,10 +1134,7 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
     }
     
     the_atoms[i]->setMass( currentAtomType->mass );
-    the_atoms[i]->setEpslon( currentAtomType->epslon );
-    the_atoms[i]->setSigma( currentAtomType->sigma );
     the_atoms[i]->setIdent( currentAtomType->ident );
-    the_atoms[i]->setLJ();
 
     if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
 
@@ -1144,19 +1142,19 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
       if( the_atoms[i]->isDirectional() ){
 	
 	dAtom = (DirectionalAtom *) the_atoms[i];
-	dAtom->setMu( currentAtomType->dipole );
 	dAtom->setHasDipole( 1 );
-	dAtom->setJx( 0.0 );
-	dAtom->setJy( 0.0 );
-	dAtom->setJz( 0.0 );
+
+        ji[0] = 0.0;
+        ji[1] = 0.0;
+        ji[2] = 0.0;
+
+        dAtom->setJ( ji );
 	
 	if(!strcmp("SSD",the_atoms[i]->getType())){
 	  dAtom->setI( waterI );
-	  dAtom->setSSD( 1 );
 	}
 	else if(!strcmp("HEAD",the_atoms[i]->getType())){
 	  dAtom->setI( headI );
-	  dAtom->setSSD( 0 );
 	}
 	else{
 	  sprintf(painCave.errMsg,
@@ -1180,7 +1178,7 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
     else{
       if( the_atoms[i]->isDirectional() ){
 	sprintf( painCave.errMsg,
-		 "DUFF error: Atom \"%s\" was given a standard"
+		 "DUFF error: Atom \"%s\" was given a standard "
 		 "orientation in the BASS file, yet it is not a dipole.\n",
 		 currentAtomType->name);
 	painCave.isFatal = 1;