--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/07/16 21:30:56	626
+++ trunk/OOPSE/libmdtools/ForceFields.cpp	2003/12/22 21:27:04	892
@@ -3,13 +3,17 @@ using namespace std;
 using namespace std;
 
 
-#include <cstdlib>
+#include <stdlib.h>
 
 #ifdef IS_MPI
 #include <mpi.h>
 #endif // is_mpi
 
 
+#ifdef PROFILE
+#include "mdProfile.hpp"
+#endif
+
 #include "simError.h"
 #include "ForceFields.hpp"
 #include "Atom.hpp"
@@ -26,7 +30,8 @@ void ForceFields::calcRcut( void ){
 
   //calc rCut and rList
 
-  entry_plug->setRcut( 2.5 * bigSigma );  
+  entry_plug->setDefaultRcut( 2.5 * bigSigma );  
+    
 }
 
 void ForceFields::doForces( int calcPot, int calcStress ){
@@ -37,7 +42,7 @@ void ForceFields::doForces( int calcPot, int calcStres
   double* trq;
   double* A;
   double* u_l;;
-  DirectionalAtom* dAtom;
+  SimState* config;
 
   short int passedCalcPot = (short int)calcPot;
   short int passedCalcStress = (short int)calcStress;
@@ -49,17 +54,25 @@ void ForceFields::doForces( int calcPot, int calcStres
     entry_plug->atoms[i]->zeroForces();    
   }
 
+#ifdef PROFILE
+  startProfile(pro7);
+#endif
+  
   for(i=0; i<entry_plug->n_mol; i++ ){
     entry_plug->molecules[i].calcForces();
   }
 
+#ifdef PROFILE
+  endProfile( pro7 );
+#endif
+
+  config = entry_plug->getConfiguration();
   
-  
-  frc = Atom::getFrcArray();
-  pos = Atom::getPosArray();
-  trq = Atom::getTrqArray();
-  A   = Atom::getAmatArray();
-  u_l = Atom::getUlArray();
+  frc = config->getFrcArray();
+  pos = config->getPosArray();
+  trq = config->getTrqArray();
+  A   = config->getAmatArray();
+  u_l = config->getUlArray();
 
   isError = 0;
   entry_plug->lrPot = 0.0;
@@ -68,6 +81,11 @@ void ForceFields::doForces( int calcPot, int calcStres
     entry_plug->tau[i] = 0.0;
   }
 
+
+#ifdef PROFILE
+  startProfile(pro8);
+#endif
+
   fortranForceLoop( pos,
 		    A,
 		    u_l,
@@ -79,6 +97,11 @@ void ForceFields::doForces( int calcPot, int calcStres
 		    &passedCalcStress,
 		    &isError );
 
+#ifdef PROFILE
+  endProfile(pro8);
+#endif
+
+
   if( isError ){
     sprintf( painCave.errMsg,
 	     "Error returned from the fortran force calculation.\n" );