--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/04/03 20:21:54	447
+++ trunk/OOPSE/libmdtools/ForceFields.cpp	2003/12/22 21:27:04	892
@@ -1,10 +1,19 @@
-#include <cstdlib>
+#include <iostream>
 
+using namespace std;
+
+
+#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"
@@ -21,16 +30,8 @@ void ForceFields::calcRcut( void ){
 
   //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;
-  
+  entry_plug->setDefaultRcut( 2.5 * bigSigma );  
+    
 }
 
 void ForceFields::doForces( int calcPot, int calcStress ){
@@ -39,68 +40,67 @@ void ForceFields::doForces( int calcPot, int calcStres
   double* frc;
   double* pos;
   double* trq;
-  double* tau;
   double* A;
   double* u_l;;
-  DirectionalAtom* dAtom;
+  SimState* config;
 
-  double ut[3];
-
-  //u_l = new double[entry_plug->n_atoms];
-
   short int passedCalcPot = (short int)calcPot;
   short int passedCalcStress = (short int)calcStress;
 
-  // forces are zeroed here, before any are acumulated.
+  // forces are zeroed here, before any are accumulated.
   // NOTE: do not rezero the forces in Fortran.
 
-
   for(i=0; i<entry_plug->n_atoms; i++){
-    entry_plug->atoms[i]->zeroForces();
-
-//     if( entry_plug->atoms[i]->isDirectional() ){
-//       dAtom = (DirectionalAtom *)entry_plug->atoms[i];
-//       dAtom->getU(ut);
-    
-
-//       if(dAtom->getIndex()== 1){
-// 	std::cerr << "atom 2's u_l = " << ut[0] << ", " << ut[1]
-// 		  << ", " << ut[2] << "\n";
-//       }
-//     }
-    
+    entry_plug->atoms[i]->zeroForces();    
   }
 
+#ifdef PROFILE
+  startProfile(pro7);
+#endif
+  
   for(i=0; i<entry_plug->n_mol; i++ ){
     entry_plug->molecules[i].calcForces();
   }
 
-  frc = Atom::getFrcArray();
-  pos = Atom::getPosArray();
-  trq = Atom::getTrqArray();
-  A   = Atom::getAmatArray();
-  u_l = Atom::getUlArray();
-  tau = entry_plug->tau;
+#ifdef PROFILE
+  endProfile( pro7 );
+#endif
 
+  config = entry_plug->getConfiguration();
   
+  frc = config->getFrcArray();
+  pos = config->getPosArray();
+  trq = config->getTrqArray();
+  A   = config->getAmatArray();
+  u_l = config->getUlArray();
+
   isError = 0;
   entry_plug->lrPot = 0.0;
 
+  for (i=0; i<9; i++) {
+    entry_plug->tau[i] = 0.0;
+  }
 
-  
+
+#ifdef PROFILE
+  startProfile(pro8);
+#endif
+
   fortranForceLoop( pos,
 		    A,
 		    u_l,
 		    frc,
 		    trq,
-		    tau,
+		    entry_plug->tau,
 		    &(entry_plug->lrPot), 
 		    &passedCalcPot,
 		    &passedCalcStress,
 		    &isError );
 
+#ifdef PROFILE
+  endProfile(pro8);
+#endif
 
-  //  delete[] u_l;
 
   if( isError ){
     sprintf( painCave.errMsg,
@@ -114,6 +114,7 @@ void ForceFields::doForces( int calcPot, int calcStres
 	   "returned from the force calculation.\n" );
   MPIcheckPoint();
 #endif // is_mpi
+  
 
 }