--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/04/03 20:21:54	447
+++ trunk/OOPSE/libmdtools/ForceFields.cpp	2004/05/01 18:52:38	1144
@@ -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 +30,45 @@ 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->setDefaultRcut( 2.5 * bigSigma );  
+    
+}
+
+void ForceFields::setRcut( double LJrcut ) {
   
-  entry_plug->rList = entry_plug->rCut + 1.0;
+#ifdef IS_MPI
+  double tempBig = bigSigma;
+  MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
+                 MPI_COMM_WORLD);
+#endif  //is_mpi
   
+  if (LJrcut < 2.5 * bigSigma) {
+    sprintf( painCave.errMsg,
+             "Setting Lennard-Jones cutoff radius to %lf.\n"
+             "\tThis value is smaller than %lf, which is\n"
+             "\t2.5 * bigSigma, where bigSigma is the largest\n"
+             "\tvalue of sigma present in the simulation.\n"
+             "\tThis is potentially a problem since the LJ potential may\n"
+             "\tbe appreciable at this distance.  If you don't want the\n"
+             "\tsmaller cutoff, change the LJrcut variable.\n",
+             LJrcut, 2.5*bigSigma);
+    painCave.isFatal = 0;
+    simError();
+  } else {
+    sprintf( painCave.errMsg,
+             "Setting Lennard-Jones cutoff radius to %lf.\n"
+             "\tThis value is larger than %lf, which is\n"
+             "\t2.5 * bigSigma, where bigSigma is the largest\n"
+             "\tvalue of sigma present in the simulation. This should\n"
+             "\tnot be a problem, but could adversely effect performance.\n",
+             LJrcut, 2.5*bigSigma);
+    painCave.isFatal = 0;
+    simError();
+  }
+  
+  //calc rCut and rList
+  
+  entry_plug->setDefaultRcut( LJrcut );
 }
 
 void ForceFields::doForces( int calcPot, int calcStress ){
@@ -39,69 +77,76 @@ void ForceFields::doForces( int calcPot, int calcStres
   double* frc;
   double* pos;
   double* trq;
-  double* tau;
   double* A;
-  double* u_l;;
-  DirectionalAtom* dAtom;
+  double* u_l;
+  double* rc;
+  double* massRatio;
+  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++ ){
+    // CalcForces in molecules takes care of mapping rigid body coordinates
+    // into atomic coordinates
     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();
+  rc = config->getRcArray();
+  massRatio = config->getMassRatioArray();
+
   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,
+  		    rc,
 		    A,
 		    u_l,
 		    frc,
 		    trq,
-		    tau,
+		    entry_plug->tau,
 		    &(entry_plug->lrPot), 
 		    &passedCalcPot,
 		    &passedCalcStress,
 		    &isError );
 
 
-  //  delete[] u_l;
+#ifdef PROFILE
+  endProfile(pro8);
+#endif
 
+
   if( isError ){
     sprintf( painCave.errMsg,
 	     "Error returned from the fortran force calculation.\n" );
@@ -109,11 +154,17 @@ void ForceFields::doForces( int calcPot, int calcStres
     simError();
   }
 
+  for(i=0; i<entry_plug->n_mol; i++ ){
+    entry_plug->molecules[i].atoms2rigidBodies();
+  }
+
+
 #ifdef IS_MPI
   sprintf( checkPointMsg,
 	   "returned from the force calculation.\n" );
   MPIcheckPoint();
 #endif // is_mpi
+  
 
 }