--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/28 22:06:29	1139
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/12 14:30:12	1163
@@ -183,7 +183,9 @@ void SimSetup::makeMolecules(void){
   BendStamp* currentBend;
   TorsionStamp* currentTorsion;
   RigidBodyStamp* currentRigidBody;
-
+  CutoffGroupStamp* currentCutoffGroup;
+  CutoffGroup* myCutoffGroup;
+  
   bond_pair* theBonds;
   bend_set* theBends;
   torsion_set* theTorsions;
@@ -216,6 +218,7 @@ void SimSetup::makeMolecules(void){
       molInfo.nBends = comp_stamps[stampID]->getNBends();
       molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
       molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
+      molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
       
       molInfo.myAtoms = &(info[k].atoms[atomOffset]);
 
@@ -479,8 +482,33 @@ void SimSetup::makeMolecules(void){
         molInfo.myRigidBodies.push_back(myRB);
         info[k].rigidBodies.push_back(myRB);
       }
+      
+
+      //create cutoff group for molecule
+      molInfo.myCutoffGroups.clear();
+      for (j = 0; j < molInfo.nCutoffGroups; j++){
+
+        currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
+        nMembers = currentCutoffGroup->getNMembers(); 
+
+        myCutoffGroup = new CutoffGroup();
+        
+        for (int cg = 0; cg < nMembers; cg++) {
+
+          // molI is atom numbering inside this molecule
+          molI = currentCutoffGroup->getMember(cg);     
+
+          // tempI is atom numbering on local processor
+          tempI = molI + atomOffset;
+
+          myCutoffGroup->addAtom(info[k].atoms[tempI]);          
+        }
+
+        molInfo.myCutoffGroups.push_back(myCutoffGroup);
+      }//end for (j = 0; j < molInfo.nCutoffGroups; j++)
       
 
+
       // After this is all set up, scan through the atoms to 
       // see if they can be added to the integrableObjects:
 
@@ -536,18 +564,6 @@ void SimSetup::makeMolecules(void){
   MPIcheckPoint();
 #endif // is_mpi
 
-  // clean up the forcefield
-
-  if (!globals->haveLJrcut()){
-
-    the_ff->calcRcut();
-
-  } else {
-    
-    the_ff->setRcut( globals->getLJrcut() );
-  }
-
-  the_ff->cleanMe();
 }
 
 void SimSetup::initFromBass(void){
@@ -911,8 +927,6 @@ void SimSetup::gatherInfo(void){
 
     info[i].useInitXSstate = globals->getUseInitXSstate();
     info[i].orthoTolerance = globals->getOrthoBoxTolerance();
-    info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
-
     
   }
   
@@ -989,39 +1003,61 @@ void SimSetup::finalInfoCheck(void){
     MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
 #endif //is_mpi
 
-    double theEcr, theEst;
+    double theRcut, theRsw;
 
+    if (globals->haveRcut()) {
+      theRcut = globals->getRcut();
+
+      if (globals->haveRsw()) 
+        theRsw = globals->getRsw();
+      else 
+        theRsw = theRcut;
+      
+      info[i].setDefaultRcut(theRcut, theRsw);
+
+    } else {
+      
+      the_ff->calcRcut();
+      theRcut = info[i].getRcut();
+
+      if (globals->haveRsw()) 
+        theRsw = globals->getRsw();
+      else 
+        theRsw = theRcut;
+      
+      info[i].setDefaultRcut(theRcut, theRsw);
+    }
+
     if (globals->getUseRF()){
       info[i].useReactionField = 1;
-
-      if (!globals->haveECR()){
+      
+      if (!globals->haveRcut()){
         sprintf(painCave.errMsg,
-                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
+                "SimSetup Warning: No value was set for the cutoffRadius.\n"
                 "\tOOPSE will use a default value of 15.0 angstroms"
-                "\tfor the electrostaticCutoffRadius.\n");
+                "\tfor the cutoffRadius.\n");
         painCave.isFatal = 0;
         simError();
-        theEcr = 15.0;
+        theRcut = 15.0;
       }
       else{
-        theEcr = globals->getECR();
+        theRcut = globals->getRcut();
       }
 
-      if (!globals->haveEST()){
+      if (!globals->haveRsw()){
         sprintf(painCave.errMsg,
-                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
+                "SimSetup Warning: No value was set for switchingRadius.\n"
                 "\tOOPSE will use a default value of\n"
-                "\t0.05 * electrostaticCutoffRadius\n"
-                "\tfor the electrostaticSkinThickness\n");
+                "\t0.95 * cutoffRadius for the switchingRadius\n");
         painCave.isFatal = 0;
         simError();
-        theEst = 0.05 * theEcr;
+        theRsw = 0.95 * theRcut;
       }
       else{
-        theEst = globals->getEST();
+        theRsw = globals->getRsw();
       }
 
-      info[i].setDefaultEcr(theEcr, theEst);
+      info[i].setDefaultRcut(theRcut, theRsw);
 
       if (!globals->haveDielectric()){
         sprintf(painCave.errMsg,
@@ -1035,34 +1071,35 @@ void SimSetup::finalInfoCheck(void){
     }
     else{
       if (usesDipoles || usesCharges){
-        if (!globals->haveECR()){
+
+        if (!globals->haveRcut()){
           sprintf(painCave.errMsg,
-                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
+                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
                   "\tOOPSE will use a default value of 15.0 angstroms"
-                  "\tfor the electrostaticCutoffRadius.\n");
-	  painCave.isFatal = 0;
-	  simError();
-	  theEcr = 15.0;
-        }
+                  "\tfor the cutoffRadius.\n");
+          painCave.isFatal = 0;
+          simError();
+          theRcut = 15.0;
+      }
         else{
-          theEcr = globals->getECR();
+          theRcut = globals->getRcut();
         }
-	
-        if (!globals->haveEST()){
-          sprintf(painCave.errMsg,
-                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
+        
+        if (!globals->haveRsw()){
+          sprintf(painCave.errMsg,
+                  "SimSetup Warning: No value was set for switchingRadius.\n"
                   "\tOOPSE will use a default value of\n"
-                  "\t0.05 * electrostaticCutoffRadius\n"
-                  "\tfor the electrostaticSkinThickness\n");
+                  "\t0.95 * cutoffRadius for the switchingRadius\n");
           painCave.isFatal = 0;
           simError();
-          theEst = 0.05 * theEcr;
+          theRsw = 0.95 * theRcut;
         }
         else{
-          theEst = globals->getEST();
+          theRsw = globals->getRsw();
         }
+        
+        info[i].setDefaultRcut(theRcut, theRsw);
 	
-        info[i].setDefaultEcr(theEcr, theEst);
       }
     }
   }
@@ -1070,6 +1107,9 @@ void SimSetup::finalInfoCheck(void){
   strcpy(checkPointMsg, "post processing checks out");
   MPIcheckPoint();
 #endif // is_mpi
+
+  // clean up the forcefield
+  the_ff->cleanMe();
 }
   
 void SimSetup::initSystemCoords(void){
@@ -1284,7 +1324,10 @@ void SimSetup::compList(void){
   LinkedMolStamp* headStamp = new LinkedMolStamp();
   LinkedMolStamp* currentStamp = NULL;
   comp_stamps = new MoleculeStamp * [n_components];
+  bool haveCutoffGroups;
 
+  haveCutoffGroups = false;
+  
   // make an array of molecule stamps that match the components used.
   // also extract the used stamps out into a separate linked list
 
@@ -1319,7 +1362,13 @@ void SimSetup::compList(void){
       headStamp->add(currentStamp);
       comp_stamps[i] = headStamp->match(id);
     }
+
+    if(comp_stamps[i]->getNCutoffGroups() > 0)
+      haveCutoffGroups = true;    
   }
+    
+  for (i = 0; i < nInfo; i++)
+    info[i].haveCutoffGroups = haveCutoffGroups;
 
 #ifdef IS_MPI
   strcpy(checkPointMsg, "Component stamps successfully extracted\n");
@@ -1494,7 +1543,7 @@ void SimSetup::makeSysArrays(void){
     info[l].atoms = the_atoms;
     info[l].molecules = the_molecules;
     info[l].nGlobalExcludes = 0;
-
+    
     the_ff->setSimInfo(info);
   }
 }