--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/03/27 20:12:15	423
+++ trunk/OOPSE/libmdtools/ForceFields.cpp	2003/10/29 17:55:28	841
@@ -1,5 +1,10 @@
-#include <cstdlib>
+#include <iostream>
 
+using namespace std;
+
+
+#include <stdlib.h>
+
 #ifdef IS_MPI
 #include <mpi.h>
 #endif // is_mpi
@@ -15,21 +20,14 @@ void ForceFields::calcRcut( void ){
 
 #ifdef IS_MPI
   double tempBig = bigSigma;
-  MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
+  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->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 ){
@@ -38,48 +36,69 @@ void ForceFields::doForces( int calcPot, int calcStres
   double* frc;
   double* pos;
   double* trq;
-  double* tau;
   double* A;
-  double* u_l;
+  double* u_l;;
+  SimState* config;
 
   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_mol; i++ ){
-    entry_plug->molecules[i]->calc_forces();
+    entry_plug->molecules[i].calcForces();
   }
 
-  frc = Atom::getFrcArray();
-  pos = Atom::getPosArray();
-  trq = Atom::getTrqArray();
-  A   = Atom::getAmatArray();
-  u_l = Atom::getUlArray();
+  config = entry_plug->getConfiguration();
+  
+  frc = config->getFrcArray();
+  pos = config->getPosArray();
+  trq = config->getTrqArray();
+  A   = config->getAmatArray();
+  u_l = config->getUlArray();
 
-  tau = entry_plug->tau;
-    
   isError = 0;
   entry_plug->lrPot = 0.0;
 
-  
+  for (i=0; i<9; i++) {
+    entry_plug->tau[i] = 0.0;
+  }
+
+  std::cerr << "before\n"
+	    << "  force[0] = " << frc[0] << "\n"
+	    << "  pos[0]   = " << pos[0] << "\n"
+	    << "  trq[0]   = " << trq[0] << "\n"
+	    << "  A[0]     = " << A[0] << "\n"
+	    << "  tau      = " << entry_plug->tau[0] << ", " << entry_plug->tau[1] << ", " << entry_plug->tau[2] << "\n"
+	    << "             " << entry_plug->tau[3] << ", " << entry_plug->tau[4] << ", " << entry_plug->tau[5] << "\n"
+	    << "             " << entry_plug->tau[6] << ", " << entry_plug->tau[7] << ", " << entry_plug->tau[8] << "\n\n"; 
+
   fortranForceLoop( pos,
 		    A,
 		    u_l,
 		    frc,
 		    trq,
-		    tau,
+		    entry_plug->tau,
 		    &(entry_plug->lrPot), 
 		    &passedCalcPot,
 		    &passedCalcStress,
 		    &isError );
 
 
+  std::cerr << "after\n"
+	    << "  force[0] = " << frc[0] << "\n"
+	    << "  pos[0]   = " << pos[0] << "\n"
+	    << "  trq[0]   = " << trq[0] << "\n"
+	    << "  A[0]     = " << A[0] << "\n"
+	    << "  tau      = " << entry_plug->tau[0] << ", " << entry_plug->tau[1] << ", " << entry_plug->tau[2] << "\n"
+	    << "             " << entry_plug->tau[3] << ", " << entry_plug->tau[4] << ", " << entry_plug->tau[5] << "\n"
+	    << "             " << entry_plug->tau[6] << ", " << entry_plug->tau[7] << ", " << entry_plug->tau[8] << "\n\n";
+
   if( isError ){
     sprintf( painCave.errMsg,
 	     "Error returned from the fortran force calculation.\n" );
@@ -92,6 +111,7 @@ void ForceFields::doForces( int calcPot, int calcStres
 	   "returned from the force calculation.\n" );
   MPIcheckPoint();
 #endif // is_mpi
+  
 
 }