--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/03/24 15:26:05	389
+++ trunk/OOPSE/libmdtools/ForceFields.cpp	2003/07/02 21:26:55	572
@@ -1,3 +1,8 @@
+#include <iostream>
+
+using namespace std;
+
+
 #include <cstdlib>
 
 #ifdef IS_MPI
@@ -11,28 +16,50 @@ void ForceFields::doForces( int calcPot, int calcStres
 #include "fortranWrappers.hpp"
 
 
+void ForceFields::calcRcut( void ){
+
+#ifdef IS_MPI
+  double tempBig = bigSigma;
+  MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
+		 MPI_COMM_WORLD);
+#endif  //is_mpi
+
+  //calc rCut and rList
+
+  entry_plug->rCut = 2.5 * bigSigma;
+  if(entry_plug->rCut > (entry_plug->boxLx / 2.0)) 
+    entry_plug->rCut = entry_plug->boxLx / 2.0;
+  if(entry_plug->rCut > (entry_plug->boxLy / 2.0)) 
+    entry_plug->rCut = entry_plug->boxLy / 2.0;
+  if(entry_plug->rCut > (entry_plug->boxLz / 2.0)) 
+    entry_plug->rCut = entry_plug->boxLz / 2.0;
+  
+  entry_plug->rList = entry_plug->rCut + 1.0;
+  
+}
+
 void ForceFields::doForces( int calcPot, int calcStress ){
 
   int i, isError;
   double* frc;
   double* pos;
   double* trq;
-  double* tau;
   double* A;
-  double* u_l;
+  double* u_l;;
+  DirectionalAtom* dAtom;
 
   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();
+    entry_plug->atoms[i]->zeroForces();    
   }
 
-  for(i=0; i<entry_plug->n_SRI; i++ ){
-    entry_plug->sr_interactions[i]->calc_forces();
+  for(i=0; i<entry_plug->n_mol; i++ ){
+    entry_plug->molecules[i].calcForces();
   }
 
   frc = Atom::getFrcArray();
@@ -41,22 +68,24 @@ void ForceFields::doForces( int calcPot, int calcStres
   A   = Atom::getAmatArray();
   u_l = Atom::getUlArray();
 
-  tau = entry_plug->tau;
-    
   isError = 0;
   entry_plug->lrPot = 0.0;
+
+  for (i=0; i<9; i++) {
+    entry_plug->tau[i] = 0.0;
+  }
+
   fortranForceLoop( pos,
 		    A,
 		    u_l,
 		    frc,
 		    trq,
-		    tau,
+		    entry_plug->tau,
 		    &(entry_plug->lrPot), 
 		    &passedCalcPot,
 		    &passedCalcStress,
 		    &isError );
 
-
   if( isError ){
     sprintf( painCave.errMsg,
 	     "Error returned from the fortran force calculation.\n" );