--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/09/22 23:07:57	781
+++ 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 +30,7 @@ void ForceFields::calcRcut( void ){
 
   //calc rCut and rList
 
-  entry_plug->setRcut( 2.5 * bigSigma );  
+  entry_plug->setDefaultRcut( 2.5 * bigSigma );  
     
 }
 
@@ -38,7 +42,6 @@ void ForceFields::doForces( int calcPot, int calcStres
   double* trq;
   double* A;
   double* u_l;;
-  DirectionalAtom* dAtom;
   SimState* config;
 
   short int passedCalcPot = (short int)calcPot;
@@ -51,10 +54,18 @@ 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 = config->getFrcArray();
@@ -70,6 +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,
@@ -81,6 +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" );