--- trunk/OOPSE/libmdtools/DUFF.cpp	2004/01/13 23:01:43	941
+++ trunk/OOPSE/libmdtools/DUFF.cpp	2004/06/02 18:27:52	1224
@@ -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();
 
     }
 
@@ -477,7 +477,7 @@ DUFF::DUFF(){
   // Init the atomStruct mpi type
 
   atomStruct atomProto; // mpiPrototype
-  int atomBC[3] = {15,11,4};  // block counts
+  int atomBC[3] = {15,12,5};  // block counts
   MPI_Aint atomDspls[3];           // displacements
   MPI_Datatype atomMbrTypes[3];    // member mpi types
 
@@ -595,10 +595,12 @@ DUFF::DUFF(){
       if( frcFile == NULL ){
 	
 	sprintf( painCave.errMsg,
-		 "Error opening the force field parameter file: %s\n"
-		 "Have you tried setting the FORCE_PARAM_PATH environment "
-		 "vairable?\n",
+		 "Error opening the force field parameter file:\n"
+                 "\t%s\n"
+		 "\tHave you tried setting the FORCE_PARAM_PATH environment "
+		 "variable?\n",
 		 fileName );
+        painCave.severity = OOPSE_ERROR;
 	painCave.isFatal = 1;
 	simError();
       }
@@ -730,8 +732,6 @@ void DUFF::readParams( void ){
     currentAtomType = headAtomType->next; //skip the first element who is a place holder.
     while( currentAtomType != NULL ){
       currentAtomType->duplicate( atomInfo );
-
- 
 
       sendFrcStruct( &atomInfo, mpiAtomStructType );
 
@@ -750,21 +750,19 @@ void DUFF::readParams( void ){
   else{
     
     // listen for node 0 to send out the force params
-    
+
     MPIcheckPoint();
 
     headAtomType = new LinkedAtomType;
-    recieveFrcStruct( &atomInfo, mpiAtomStructType );
+    receiveFrcStruct( &atomInfo, mpiAtomStructType );
     
     while( !atomInfo.last ){
 
-
-
       headAtomType->add( atomInfo );
       
       MPIcheckPoint();
 
-      recieveFrcStruct( &atomInfo, mpiAtomStructType );
+      receiveFrcStruct( &atomInfo, mpiAtomStructType );
     }
   }
 
@@ -898,11 +896,11 @@ void DUFF::readParams( void ){
     MPIcheckPoint(); 
 
     headBondType = new LinkedBondType;
-    recieveFrcStruct( &bondInfo, mpiBondStructType );
+    receiveFrcStruct( &bondInfo, mpiBondStructType );
     while( !bondInfo.last ){
 
       headBondType->add( bondInfo );
-      recieveFrcStruct( &bondInfo, mpiBondStructType );
+      receiveFrcStruct( &bondInfo, mpiBondStructType );
     }
   }
 
@@ -926,7 +924,7 @@ void DUFF::readParams( void ){
     fastForward( "BendTypes", "initializeBends" );
 
     // we are now at the bendTypes section
-
+    
     eof_test =  fgets( readLine, sizeof(readLine), frcFile );
     lineNum++;
         
@@ -981,11 +979,11 @@ void DUFF::readParams( void ){
     MPIcheckPoint();
 
     headBendType = new LinkedBendType;
-    recieveFrcStruct( &bendInfo, mpiBendStructType );
+    receiveFrcStruct( &bendInfo, mpiBendStructType );
     while( !bendInfo.last ){
 
       headBendType->add( bendInfo );
-      recieveFrcStruct( &bendInfo, mpiBendStructType );
+      receiveFrcStruct( &bendInfo, mpiBendStructType );
     }
   }
 
@@ -1066,11 +1064,11 @@ void DUFF::readParams( void ){
     MPIcheckPoint();
 
     headTorsionType = new LinkedTorsionType;
-    recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
+    receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
     while( !torsionInfo.last ){
 
       headTorsionType->add( torsionInfo );
-      recieveFrcStruct( &torsionInfo, mpiTorsionStructType );
+      receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
     }
   }
 
@@ -1124,6 +1122,7 @@ void DUFF::initializeAtoms( int nAtoms, Atom** the_ato
   // initialize the atoms
   
   DirectionalAtom* dAtom;
+  double ji[3];
 
   for(int i=0; i<nAtoms; i++ ){
 
@@ -1137,10 +1136,7 @@ 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;
 
@@ -1148,19 +1144,19 @@ 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,
@@ -1184,7 +1180,7 @@ 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;