--- trunk/OOPSE/libmdtools/DUFF.cpp	2003/07/17 19:25:51	631
+++ trunk/OOPSE/libmdtools/DUFF.cpp	2003/10/28 16:03:37	829
@@ -1,6 +1,6 @@
-#include <cstdlib>
-#include <cstdio>
-#include <cstring>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
 
 #include <iostream>
 using namespace std;
@@ -35,6 +35,11 @@ namespace DUFF_NS {  // restrict the access of the fol
     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 DUFF_NS {  // restrict the access of the fol
 	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 DUFF_NS {  // restrict the access of the fol
       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 DUFF_NS {  // restrict the access of the fol
     double dipole;
     double w0;
     double v0;
+    double v0p;
+    double rl;
+    double ru;
+    double rlp;
+    double rup;
     int ident;
     LinkedAtomType* next;
   };
@@ -434,7 +454,6 @@ DUFF::DUFF(){
   char* ffPath_env = "FORCE_PARAM_PATH";
   char* ffPath;
   char temp[200];
-  char errMsg[1000];
 
   headAtomType       = NULL; 
   currentAtomType    = NULL;
@@ -456,7 +475,7 @@ DUFF::DUFF(){
   // Init the atomStruct mpi type
 
   atomStruct atomProto; // mpiPrototype
-  int atomBC[3] = {15,6,4};  // block counts
+  int atomBC[3] = {15,11,4};  // block counts
   MPI_Aint atomDspls[3];           // displacements
   MPI_Datatype atomMbrTypes[3];    // member mpi types
 
@@ -638,12 +657,7 @@ void DUFF::readParams( void ){
 
 void DUFF::readParams( void ){
 
-  int i, a, b, c, d;
   int identNum;
-  char* atomA;
-  char* atomB;
-  char* atomC;
-  char* atomD;
   
   atomStruct atomInfo;
   bondStruct bondInfo;
@@ -765,16 +779,17 @@ void DUFF::readParams( void ){
   int isGB = 0;
   int isLJ = 1;
   int isEAM =0;
-  double GB_dummy = 0.0;
-  
-  
+    
   currentAtomType = headAtomType->next;;
   while( currentAtomType != NULL ){
     
     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' ){
@@ -1287,7 +1302,8 @@ void DUFF::initializeBends( int nBends, Bend** bendArr
 	}
 	
 	gBend = new GhostBend( *the_atoms[a], 
-			       *the_atoms[b] );			       
+			       *the_atoms[b]);
+			       			      		       
 	gBend->setConstants( currentBendType->k1,
 			     currentBendType->k2,
 			     currentBendType->k3,
@@ -1303,7 +1319,7 @@ void DUFF::initializeBends( int nBends, Bend** bendArr
 			     currentBendType->k3,
 			     currentBendType->t0 );
 	bendArray[i] = qBend;
-      }
+      }      
     }
   }
 }
@@ -1496,8 +1512,52 @@ int DUFF_NS::parseAtom( char *lineBuffer, int lineNum,
       }
       
       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;
   }
@@ -1543,6 +1603,8 @@ int DUFF_NS::parseBond( char *lineBuffer, int lineNum,
       }
       
       info.d0 = atof( the_token );
+      
+      info.k0=0.0;
     }
     else if( !strcmp( bondType, "harmonic" ) ){
       info.type = HARMONIC_BOND;
@@ -1569,7 +1631,7 @@ int DUFF_NS::parseBond( char *lineBuffer, int lineNum,
     else{
       sprintf( painCave.errMsg, 
 	       "Unknown DUFF bond type \"%s\" at line %d\n",
-	       info.type,
+	       bondType,
 	       lineNum );
       painCave.isFatal = 1;
       simError();