--- trunk/src/brains/SimInfo.cpp	2005/03/09 17:30:29	413
+++ trunk/src/brains/SimInfo.cpp	2005/03/11 15:00:20	432
@@ -367,7 +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) {
@@ -412,6 +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);
+            }
+        }
+    }  
+
 }
 
 
@@ -646,9 +697,6 @@ void SimInfo::setupFortranSim() {
     }
     
     //setup fortran simulation
-    //gloalExcludes and molMembershipArray should go away (They are never used)
-    //why the hell fortran need to know molecule?
-    //OOPSE = Object-Obfuscated Parallel Simulation Engine
     int nGlobalExcludes = 0;
     int* globalExcludes = NULL; 
     int* excludeList = exclude_.getExcludeList();
@@ -836,11 +884,10 @@ void SimInfo::setSnapshotManager(SnapshotManager* sman
 }
 
 void SimInfo::setSnapshotManager(SnapshotManager* sman) {
-    //if (sman_ == sman_) {
-    //    return;
-    //}
-    
-    //delete sman_;
+    if (sman_ == sman) {
+        return;
+    }    
+    delete sman_;
     sman_ = sman;
 
     Molecule* mol;