--- trunk/OOPSE/libmdtools/ForceFields.cpp	2003/12/22 21:27:04	892
+++ trunk/OOPSE/libmdtools/ForceFields.cpp	2004/05/12 16:38:45	1167
@@ -34,16 +34,67 @@ void ForceFields::doForces( int calcPot, int calcStres
     
 }
 
+void ForceFields::setRcut( double LJrcut ) {
+  
+#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 ){
 
-  int i, isError;
+  int i, j, isError;
   double* frc;
   double* pos;
   double* trq;
   double* A;
-  double* u_l;;
+  double* u_l;
+  double* rc;
+  double* massRatio;
   SimState* config;
 
+  Molecule* myMols;
+  Atom** myAtoms;
+  int numAtom;
+  int curIndex;
+  double mtot;
+  int numMol;
+  int numCutoffGroups;
+  CutoffGroup* myCutoffGroup;
+  vector<CutoffGroup*>::iterator iterCutoff;
+  double com[3];
+  vector<double> rcGroup;
+  
   short int passedCalcPot = (short int)calcPot;
   short int passedCalcStress = (short int)calcStress;
 
@@ -59,7 +110,9 @@ void ForceFields::doForces( int calcPot, int calcStres
 #endif
   
   for(i=0; i<entry_plug->n_mol; i++ ){
-    entry_plug->molecules[i].calcForces();
+    // CalcForces in molecules takes care of mapping rigid body coordinates
+    // into atomic coordinates
+    entry_plug->molecules[i].calcForces();    
   }
 
 #ifdef PROFILE
@@ -74,6 +127,34 @@ void ForceFields::doForces( int calcPot, int calcStres
   A   = config->getAmatArray();
   u_l = config->getUlArray();
 
+  if(entry_plug->haveCutoffGroups){
+    myMols = entry_plug->molecules;
+    numMol = entry_plug->n_mol;
+    for(int i  = 0; i < numMol; i++){
+        
+      numCutoffGroups = myMols[i].getNCutoffGroups();
+      for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; 
+                                                    myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
+        //get center of mass of the cutoff group
+        myCutoffGroup->getCOM(com); 
+
+        rcGroup.push_back(com[0]);
+        rcGroup.push_back(com[1]);
+        rcGroup.push_back(com[2]);
+        
+      }// end for(myCutoffGroup)
+      
+    }//end for(int i = 0)
+
+    rc = &rcGroup[0];
+  }
+  else{
+    // center of mass of the group is the same as position of the atom  if cutoff group does not exist
+    rc = pos;
+  }
+  
+
+
   isError = 0;
   entry_plug->lrPot = 0.0;
 
@@ -87,6 +168,7 @@ void ForceFields::doForces( int calcPot, int calcStres
 #endif
 
   fortranForceLoop( pos,
+  		    rc,
 		    A,
 		    u_l,
 		    frc,
@@ -97,6 +179,7 @@ void ForceFields::doForces( int calcPot, int calcStres
 		    &passedCalcStress,
 		    &isError );
 
+
 #ifdef PROFILE
   endProfile(pro8);
 #endif
@@ -109,6 +192,11 @@ 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" );