--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/07/14 21:28:54	597
+++ trunk/OOPSE/libmdtools/ForceFields.cpp	2004/04/12 20:32:20	1097
@@ -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"
@@ -26,16 +30,45 @@ void ForceFields::calcRcut( void ){
 
   //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->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 ){
@@ -46,7 +79,7 @@ void ForceFields::doForces( int calcPot, int calcStres
   double* trq;
   double* A;
   double* u_l;;
-  DirectionalAtom* dAtom;
+  SimState* config;
 
   short int passedCalcPot = (short int)calcPot;
   short int passedCalcStress = (short int)calcStress;
@@ -58,17 +91,27 @@ 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++ ){
+    // CalcForces in molecules takes care of mapping rigid body coordinates
+    // into atomic coordinates
     entry_plug->molecules[i].calcForces();
   }
 
+#ifdef PROFILE
+  endProfile( pro7 );
+#endif
+
+  config = entry_plug->getConfiguration();
   
-  
-  frc = Atom::getFrcArray();
-  pos = Atom::getPosArray();
-  trq = Atom::getTrqArray();
-  A   = Atom::getAmatArray();
-  u_l = Atom::getUlArray();
+  frc = config->getFrcArray();
+  pos = config->getPosArray();
+  trq = config->getTrqArray();
+  A   = config->getAmatArray();
+  u_l = config->getUlArray();
 
   isError = 0;
   entry_plug->lrPot = 0.0;
@@ -77,6 +120,11 @@ void ForceFields::doForces( int calcPot, int calcStres
     entry_plug->tau[i] = 0.0;
   }
 
+
+#ifdef PROFILE
+  startProfile(pro8);
+#endif
+
   fortranForceLoop( pos,
 		    A,
 		    u_l,
@@ -88,6 +136,11 @@ 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" );
@@ -95,6 +148,11 @@ 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" );