--- trunk/OOPSE/libmdtools/DUFF.cpp	2003/06/24 19:57:54	564
+++ trunk/OOPSE/libmdtools/DUFF.cpp	2003/08/20 19:11:51	704
@@ -22,7 +22,7 @@ using namespace std;
 #define HARMONIC_BOND 1
 
 
-namespace TPE {  // restrict the access of the folowing to this file only.
+namespace DUFF_NS {  // restrict the access of the folowing to this file only.
 
 
   // Declare the structures that will be passed by MPI
@@ -35,6 +35,11 @@ namespace TPE {  // restrict the access of the folowin
     double dipole;
     double w0;
     double v0;
+    double v0p;
+    double rl;
+    double ru;
+    double rlp;
+    double rup;
     int isSSD;
     int isDipole;
     int ident;
@@ -138,6 +143,11 @@ namespace TPE {  // restrict the access of the folowin
 	next->dipole   = info.dipole;
 	next->w0       = info.w0;
 	next->v0       = info.v0;
+	next->v0p      = info.v0p;
+	next->rl       = info.rl;
+	next->ru       = info.ru;
+	next->rlp      = info.rlp;
+	next->rup      = info.rup;
 	next->ident    = info.ident;
       }
     }
@@ -154,6 +164,11 @@ namespace TPE {  // restrict the access of the folowin
       info.dipole   = dipole;
       info.w0       = w0;
       info.v0       = v0;
+      info.v0p      = v0p;
+      info.rl       = rl;
+      info.ru       = ru;
+      info.rlp      = rlp;
+      info.rup      = rup;
       info.ident    = ident;
       info.last     = 0;
     }
@@ -170,6 +185,11 @@ namespace TPE {  // restrict the access of the folowin
     double dipole;
     double w0;
     double v0;
+    double v0p;
+    double rl;
+    double ru;
+    double rlp;
+    double rup;
     int ident;
     LinkedAtomType* next;
   };
@@ -420,7 +440,7 @@ namespace TPE {  // restrict the access of the folowin
 
 } // namespace
 
-using namespace TPE;
+using namespace DUFF_NS;
 
 
 //****************************************************************
@@ -764,6 +784,7 @@ void DUFF::readParams( void ){
   
   int isGB = 0;
   int isLJ = 1;
+  int isEAM =0;
   double GB_dummy = 0.0;
   
   
@@ -773,7 +794,10 @@ void DUFF::readParams( void ){
     if(currentAtomType->isDipole) entry_plug->useDipole = 1;
     if(currentAtomType->isSSD) {
       entry_plug->useSticky = 1;
-      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0));
+      set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), 
+                         &(currentAtomType->v0p), 
+                         &(currentAtomType->rl), &(currentAtomType->ru), 
+                         &(currentAtomType->rlp), &(currentAtomType->rup));
     }
 
     if( currentAtomType->name[0] != '\0' ){
@@ -783,6 +807,7 @@ void DUFF::readParams( void ){
 		 &(currentAtomType->isSSD),
 		 &(currentAtomType->isDipole),
 		 &isGB,
+		 &isEAM,
 		 &(currentAtomType->epslon),
 		 &(currentAtomType->sigma),
 		 &(currentAtomType->dipole),
@@ -1285,7 +1310,9 @@ void DUFF::initializeBends( int nBends, Bend** bendArr
 	}
 	
 	gBend = new GhostBend( *the_atoms[a], 
-			       *the_atoms[b] );			       
+			       *the_atoms[b],
+			       *the_atoms[c] );	
+			       			      		       
 	gBend->setConstants( currentBendType->k1,
 			     currentBendType->k2,
 			     currentBendType->k3,
@@ -1301,7 +1328,7 @@ void DUFF::initializeBends( int nBends, Bend** bendArr
 			     currentBendType->k3,
 			     currentBendType->t0 );
 	bendArray[i] = qBend;
-      }
+      }      
     }
   }
 }
@@ -1408,7 +1435,7 @@ void DUFF::fastForward( char* stopText, char* searchOw
 }
 
 
-int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
+int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
  
   char* the_token;
   
@@ -1494,15 +1521,59 @@ int TPE::parseAtom( char *lineBuffer, int lineNum, ato
       }
       
       info.v0 = atof( the_token );
+      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
+	sprintf( painCave.errMsg, 
+		 "Error parseing AtomTypes: line %d\n", lineNum );
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      info.v0p = atof( the_token );
+
+      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
+	sprintf( painCave.errMsg, 
+		 "Error parseing AtomTypes: line %d\n", lineNum );
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      info.rl = atof( the_token );
+
+      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
+	sprintf( painCave.errMsg, 
+		 "Error parseing AtomTypes: line %d\n", lineNum );
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      info.ru = atof( the_token );
+
+      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
+	sprintf( painCave.errMsg, 
+		 "Error parseing AtomTypes: line %d\n", lineNum );
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      info.rlp = atof( the_token );
+
+      if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
+	sprintf( painCave.errMsg, 
+		 "Error parseing AtomTypes: line %d\n", lineNum );
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      info.rup = atof( the_token );
     }
-    else info.v0 = info.w0 = 0.0;
+    else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0;
 
     return 1;
   }
   else return 0;
 }
 
-int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
+int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
  
   char* the_token;
   char bondType[30];
@@ -1541,6 +1612,8 @@ int TPE::parseBond( char *lineBuffer, int lineNum, bon
       }
       
       info.d0 = atof( the_token );
+      
+      info.k0=0.0;
     }
     else if( !strcmp( bondType, "harmonic" ) ){
       info.type = HARMONIC_BOND;
@@ -1579,7 +1652,7 @@ int TPE::parseBond( char *lineBuffer, int lineNum, bon
 }
 
 
-int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
+int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
 
   char* the_token;
   
@@ -1667,7 +1740,7 @@ int TPE::parseBend( char *lineBuffer, int lineNum, ben
   else return 0;
 }
 
-int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
+int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
   
   char*  the_token;