--- trunk/src/brains/SimInfo.cpp	2005/02/13 20:05:42	326
+++ trunk/src/brains/SimInfo.cpp	2005/03/10 23:56:42	430
@@ -73,7 +73,7 @@ SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
                                 nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
                                 nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
                                 nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
-                                sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
+                                sman_(NULL), fortranInitialized_(false) {
 
             
     std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
@@ -139,19 +139,20 @@ SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
     molToProcMap_.resize(nGlobalMols_);
 #endif
 
-    selectMan_ = new SelectionManager(this);
-    selectMan_->selectAll();
 }
 
 SimInfo::~SimInfo() {
-    //MemoryUtils::deleteVectorOfPointer(molecules_);
-
-    MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
+    std::map<int, Molecule*>::iterator i;
+    for (i = molecules_.begin(); i != molecules_.end(); ++i) {
+        delete i->second;
+    }
+    molecules_.clear();
     
+    MemoryUtils::deletePointers(moleculeStamps_);
+    
     delete sman_;
     delete simParams_;
     delete forceField_;
-    delete selectMan_;
 }
 
 int SimInfo::getNGlobalConstraints() {
@@ -366,7 +367,32 @@ void SimInfo::addExcludePairs(Molecule* mol) {
         exclude_.addPair(c, d);        
     }
 
-    
+    Molecule::RigidBodyIterator rbIter;
+    RigidBody* rb;
+    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+        std::vector<Atom*> atoms = rb->getAtoms();
+        for (int i = 0; i < atoms.size() -1 ; ++i) {
+            for (int j = i + 1; j < atoms.size(); ++j) {
+                a = atoms[i]->getGlobalIndex();
+                b = atoms[j]->getGlobalIndex();
+                exclude_.addPair(a, b);
+            }
+        }
+    }        
+
+    Molecule::CutoffGroupIterator cgIter;
+    CutoffGroup* cg;
+    for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
+        std::vector<Atom*> atoms = cg->getAtoms();
+        for (int i = 0; i < atoms.size() -1 ; ++i) {
+            for (int j = i + 1; j < atoms.size(); ++j) {
+                a = atoms[i]->getGlobalIndex();
+                b = atoms[j]->getGlobalIndex();
+                exclude_.addPair(a, b);
+            }
+        }
+    }  
+
 }
 
 void SimInfo::removeExcludePairs(Molecule* mol) {
@@ -411,6 +437,32 @@ void SimInfo::removeExcludePairs(Molecule* mol) {
         exclude_.removePair(c, d);        
     }
 
+    Molecule::RigidBodyIterator rbIter;
+    RigidBody* rb;
+    for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
+        std::vector<Atom*> atoms = rb->getAtoms();
+        for (int i = 0; i < atoms.size() -1 ; ++i) {
+            for (int j = i + 1; j < atoms.size(); ++j) {
+                a = atoms[i]->getGlobalIndex();
+                b = atoms[j]->getGlobalIndex();
+                exclude_.removePair(a, b);
+            }
+        }
+    }        
+
+    Molecule::CutoffGroupIterator cgIter;
+    CutoffGroup* cg;
+    for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
+        std::vector<Atom*> atoms = cg->getAtoms();
+        for (int i = 0; i < atoms.size() -1 ; ++i) {
+            for (int j = i + 1; j < atoms.size(); ++j) {
+                a = atoms[i]->getGlobalIndex();
+                b = atoms[j]->getGlobalIndex();
+                exclude_.removePair(a, b);
+            }
+        }
+    }  
+
 }
 
 
@@ -765,9 +817,9 @@ void SimInfo::getCutoff(double& rcut, double& rsw) {
                 "\tfor the cutoffRadius.\n");
             painCave.isFatal = 0;
             simError();
-            rcut_ = 15.0;
+            rcut = 15.0;
         } else{
-            rcut_ = simParams_->getRcut();
+            rcut = simParams_->getRcut();
         }
 
         if (!simParams_->haveRsw()){
@@ -777,9 +829,9 @@ void SimInfo::getCutoff(double& rcut, double& rsw) {
                 "\t0.95 * cutoffRadius for the switchingRadius\n");
             painCave.isFatal = 0;
             simError();
-            rsw_ = 0.95 * rcut_;
+            rsw = 0.95 * rcut;
         } else{
-            rsw_ = simParams_->getRsw();
+            rsw = simParams_->getRsw();
         }
 
     } else {
@@ -787,16 +839,16 @@ void SimInfo::getCutoff(double& rcut, double& rsw) {
         //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
         
         if (simParams_->haveRcut()) {
-            rcut_ = simParams_->getRcut();
+            rcut = simParams_->getRcut();
         } else {
             //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
-            rcut_ = calcMaxCutoffRadius();
+            rcut = calcMaxCutoffRadius();
         }
 
         if (simParams_->haveRsw()) {
-            rsw_  = simParams_->getRsw();
+            rsw  = simParams_->getRsw();
         } else {
-            rsw_ = rcut_;
+            rsw = rcut;
         }
     
     }
@@ -835,6 +887,11 @@ void SimInfo::setSnapshotManager(SnapshotManager* sman
 }
 
 void SimInfo::setSnapshotManager(SnapshotManager* sman) {
+    //if (sman_ == sman_) {
+    //    return;
+    //}
+    
+    //delete sman_;
     sman_ = sman;
 
     Molecule* mol;