--- trunk/mdtools/interface_implementation/LJ_FF.cpp	2003/01/22 21:45:20	240
+++ trunk/mdtools/interface_implementation/LJ_FF.cpp	2003/02/04 20:15:48	263
@@ -9,7 +9,6 @@ using namespace std;
 #include "SRI.hpp"
 #include "simError.h"
 
-
 // Declare the structures that will be passed by the parser and  MPI
 
 typedef struct{
@@ -25,7 +24,6 @@ int parseAtomLJ( char *lineBuffer, int lineNum, atomSt
 int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info );
 
 #ifdef IS_MPI
-
 #include "mpiForceField.h"
 
 MPI_Datatype mpiAtomStructType;
@@ -64,7 +62,7 @@ void (*initLJfortran) ( int *nLocal, int *identArray, 
 void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma,
 		   int* status );
 
-void (*initLJfortran) ( int *nLocal, int *identArray, int *isError )
+void (*initLJfortran) ( int *nLocal, int *identArray, int *isError );
 
 LJ_FF* currentLJwrap;
 
@@ -73,6 +71,7 @@ LJ_FF::LJ_FF(){
 // begins the actual forcefield stuff.	
 //****************************************************************
 
+
 LJ_FF::LJ_FF(){
 
   char fileName[200];
@@ -207,15 +206,15 @@ 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 );
 }
 
 
@@ -242,7 +241,7 @@ 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 );
@@ -307,7 +306,7 @@ void LJ_FF::initializeAtoms( void ){
 
     headAtomType = new LinkedType;
     
-    fastFoward( "AtomTypes", "initializeAtoms" );
+    fastForward( "AtomTypes", "initializeAtoms" );
 
     // we are now at the AtomTypes section.
     
@@ -351,10 +350,19 @@ void LJ_FF::initializeAtoms( void ){
 	     "LJ_FF atom structures read successfully." );
     MPIcheckPoint();
 
-    currentAtomType = headAtomType;
+    currentAtomType = headAtomType->next; //skip the first element who is a place holder.
     while( currentAtomType != NULL ){
       currentAtomType->duplicate( info );
+
+ 
+
       sendFrcStruct( &info, mpiAtomStructType );
+
+      sprintf( checkPointMsg,
+	       "successfully sent lJ force type: \"%s\"\n",
+	       info.name );
+      MPIcheckPoint();
+
       currentAtomType = currentAtomType->next;
     }
     info.last = 1;
@@ -370,9 +378,15 @@ void LJ_FF::initializeAtoms( void ){
 
     headAtomType = new LinkedType;
     recieveFrcStruct( &info, mpiAtomStructType );
+    
     while( !info.last ){
 
+
+
       headAtomType->add( info );
+      
+      MPIcheckPoint();
+
       recieveFrcStruct( &info, mpiAtomStructType );
     }
   }
@@ -386,7 +400,7 @@ void LJ_FF::initializeAtoms( void ){
     
     if( currentAtomType->name[0] != '\0' ){
       isError = 0;
-      newLJtype( &(currentAtomType->ident),
+          newLJtype( &(currentAtomType->ident),
 		 &(currentAtomType->mass),
 		 &(currentAtomType->epslon),
 		 &(currentAtomType->sigma),
@@ -412,6 +426,7 @@ void LJ_FF::initializeAtoms( void ){
 
   // initialize the atoms
   
+  double bigSigma = 0.0;
   Atom* thisAtom;
 
   for( i=0; i<nAtoms; i++ ){
@@ -430,8 +445,24 @@ 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
   
@@ -443,6 +474,7 @@ void LJ_FF::initializeAtoms( void ){
 #endif // is_mpi
 
   initFortran();
+  entry_plug->refreshSim();
 
 }
 
@@ -587,13 +619,12 @@ 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.
@@ -605,7 +636,13 @@ 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 ){
@@ -618,7 +655,7 @@ void LJ_FF::initFortran( void ){
   ident = new int[nLocal];
 
   for(i=0; i<nLocal; i++){
-    ident[i] = entryplug->atoms[i]->getIdent();
+    ident[i] = entry_plug->atoms[i]->getIdent();
   }
 
   isError = 0;