--- trunk/mdtools/interface_implementation/LJ_FF.cpp	2003/01/17 21:53:36	238
+++ trunk/mdtools/interface_implementation/LJ_FF.cpp	2003/01/30 15:20:21	253
@@ -43,7 +43,9 @@ extern "C" {
 							double* epslon, 
 							double* sigma, 
 							int* status ),
-					    void (*p2)( void ),
+					    void (*p2)( int *nLocal,
+							int *identArray,
+							int *isError ),
 					    void (*p3)( double* positionArray,
 							double* forceArray,
 							double* potentialEnergy,
@@ -54,7 +56,7 @@ void LJfunctionWrapper( void (*p1)( int* ident, double
 
 void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, 
 				   double* sigma, int* status ),
-			void (*p2)( void ),
+			void (*p2)( int *nLocal, int *identArray, int *isError ),
 			void (*p3)( double* positionArray,double* forceArray,
 				    double* potentialEnergy,
 				    short int* doPotentialCalc ) );
@@ -62,7 +64,7 @@ void (*initLJfortran)( void );
 void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma,
 		   int* status );
 
-void (*initLJfortran)( void );
+void (*initLJfortran) ( int *nLocal, int *identArray, int *isError );
 
 LJ_FF* currentLJwrap;
 
@@ -205,15 +207,15 @@ void LJfunctionWrapper( void (*p1)( int* ident, double
 
 void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, 
 				   double* sigma, int* status ),
-			void (*p2)( void ),
+			void (*p2)( int*, int*, int* ),
 			void (*p3)( double* positionArray,double* forceArray,
 				    double* potentialEnergy,
 				    short int* doPotentialCalc ) ){
   
   
-  p1 = newLJtype;
-  p2 = initLJfortran;
-  this->setLJfortran( p3 );
+  newLJtype = p1;
+  initLJfortran = p2;
+  currentLJwrap->setLJfortran( p3 );
 }
 
 
@@ -240,7 +242,7 @@ void LJ_FF::initializeAtoms( void ){
       // check for duplicates
       
       if( !strcmp( info.name, name ) ){
-	sprintf( simError.painCave,
+	sprintf( painCave.errMsg,
 		 "Duplicate LJ atom type \"%s\" found in "
 		 "the LJ_FF param file./n",
 		 name );
@@ -305,7 +307,7 @@ void LJ_FF::initializeAtoms( void ){
 
     headAtomType = new LinkedType;
     
-    fastFoward( "AtomTypes", "initializeAtoms" );
+    fastForward( "AtomTypes", "initializeAtoms" );
 
     // we are now at the AtomTypes section.
     
@@ -382,13 +384,13 @@ void LJ_FF::initializeAtoms( void ){
   currentAtomType = headAtomType;
   while( currentAtomType != NULL ){
     
-    if( currentAtomType->name[0] != NULL ){
+    if( currentAtomType->name[0] != '\0' ){
       isError = 0;
-      newLJtype( &(currentAtomType->ident),
+          newLJtype( &(currentAtomType->ident),
 		 &(currentAtomType->mass),
 		 &(currentAtomType->epslon),
 		 &(currentAtomType->sigma),
-		 isError );
+		 &isError );
       if( isError ){
 	sprintf( painCave.errMsg,
 		 "Error initializing the \"%s\" atom type in fortran\n",
@@ -410,6 +412,7 @@ void LJ_FF::initializeAtoms( void ){
 
   // initialize the atoms
   
+  double bigSigma = 0.0;
   Atom* thisAtom;
 
   for( i=0; i<nAtoms; i++ ){
@@ -428,9 +431,25 @@ void LJ_FF::initializeAtoms( void ){
     the_atoms[i]->setSigma( currentAtomType->sigma );
     the_atoms[i]->setIdent( currentAtomType->ident );
     the_atoms[i]->setLJ();
+
+    if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
   }
 
+  
+#ifdef IS_MPI
+  double tempBig = bigSigma;
+  MPI::COMM_WORLD::Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
+#endif  //is_mpi
 
+  //calc rCut and rList
+
+  entry_plug->rCut = 2.5 * bigSigma;
+  if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0;
+  if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0;
+  if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0;
+
+  entry_plug->rList = entry_plug->rCut + 1.0;
+
   // clean up the memory
   
   delete headAtomType;
@@ -439,6 +458,9 @@ void LJ_FF::initializeAtoms( void ){
   sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" );
   MPIcheckPoint();
 #endif // is_mpi
+
+  initFortran();
+  entry_plug->refreshSim();
 
 }
 
@@ -583,13 +605,12 @@ void LJ_FF::doForces( void ){
 }
 
 
-void LJ_FF::doForces( void ){
+void LJ_FF::doForces( int calcPot ){
 
   int i;
   double* frc;
   double* pos;
-  double potE;
-  short int calcPot = 0;
+  short int passedCalcPot = (short int)calcPot;
 
   // forces are zeroed here, before any are acumulated.
   // NOTE: do not rezero the forces in Fortran.
@@ -601,6 +622,45 @@ void LJ_FF::doForces( void ){
   frc = Atom::getFrcArray();
   pos = Atom::getPosArray();
 
-  doLJfortran( pos, frc, potE, calcPot );
+//   entry_plug->lrPot = -1;
+  doLJfortran( pos, frc, &(entry_plug->lrPot), &passedCalcPot );
+
+
+ //  fprintf( stderr, 
+// 	   "lrPot =  %lf\n", entry_plug->lrPot );
+  
 }
   
+void LJ_FF::initFortran( void ){
+  
+  int nLocal = entry_plug->n_atoms;
+  int *ident;
+  int isError;
+  int i;
+
+  ident = new int[nLocal];
+
+  for(i=0; i<nLocal; i++){
+    ident[i] = entry_plug->atoms[i]->getIdent();
+  }
+
+  isError = 0;
+  initLJfortran( &nLocal, ident, &isError );
+  
+  if(isError){
+    sprintf( painCave.errMsg,
+	     "LJ_FF error: There was an error initializing the component list in fortran.\n" );
+    painCave.isFatal = 1;
+    simError();
+  }
+
+  
+#ifdef IS_MPI
+  sprintf( checkPointMsg, "LJ_FF successfully initialized the fortran component list.\n" );
+  MPIcheckPoint();
+#endif // is_mpi
+  
+  delete[] ident;
+
+}
+