--- trunk/OOPSE/libmdtools/DUFF.cpp	2003/10/28 16:03:37	829
+++ trunk/OOPSE/libmdtools/DUFF.cpp	2004/04/12 20:32:20	1097
@@ -32,6 +32,7 @@ namespace DUFF_NS {  // restrict the access of the fol
     double mass;
     double epslon;
     double sigma;
+    double charge;
     double dipole;
     double w0;
     double v0;
@@ -41,6 +42,7 @@ namespace DUFF_NS {  // restrict the access of the fol
     double rlp;
     double rup;
     int isSSD;
+    int isCharge;
     int isDipole;
     int ident;
     int last;      //  0  -> default
@@ -114,7 +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();
 
     }
 
@@ -475,7 +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
 
@@ -728,8 +730,6 @@ 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 );
 
@@ -748,21 +748,19 @@ 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 );
     }
   }
 
@@ -779,11 +777,13 @@ void DUFF::readParams( void ){
   int isGB = 0;
   int isLJ = 1;
   int isEAM =0;
+  int isCharge = 0;
+  double charge=0.0;
     
   currentAtomType = headAtomType->next;;
   while( currentAtomType != NULL ){
     
-    if(currentAtomType->isDipole) entry_plug->useDipole = 1;
+    if(currentAtomType->isDipole) entry_plug->useDipoles = 1;
     if(currentAtomType->isSSD) {
       entry_plug->useSticky = 1;
       set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), 
@@ -800,8 +800,10 @@ void DUFF::readParams( void ){
 		 &(currentAtomType->isDipole),
 		 &isGB,
 		 &isEAM,
+		 &isCharge,
 		 &(currentAtomType->epslon),
 		 &(currentAtomType->sigma),
+		 &charge,
 		 &(currentAtomType->dipole),
 		 &isError );
       if( isError ){
@@ -892,11 +894,11 @@ 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 );
     }
   }
 
@@ -920,7 +922,7 @@ void DUFF::readParams( void ){
     fastForward( "BendTypes", "initializeBends" );
 
     // we are now at the bendTypes section
-
+    
     eof_test =  fgets( readLine, sizeof(readLine), frcFile );
     lineNum++;
         
@@ -975,11 +977,11 @@ 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 );
     }
   }
 
@@ -1060,11 +1062,11 @@ 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 );
     }
   }
 
@@ -1118,6 +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++ ){
 
@@ -1131,10 +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;
 
@@ -1142,19 +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,
@@ -1178,7 +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;