--- trunk/src/brains/SimInfo.cpp	2005/03/10 23:56:42	430
+++ trunk/src/brains/SimInfo.cpp	2005/04/13 18:41:17	490
@@ -65,9 +65,9 @@ namespace oopse {
 
 namespace oopse {
 
-SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, 
+SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, 
                                 ForceField* ff, Globals* simParams) : 
-                                forceField_(ff), simParams_(simParams), 
+                                stamps_(stamps), forceField_(ff), simParams_(simParams), 
                                 ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
                                 nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), 
                                 nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
@@ -147,9 +147,8 @@ SimInfo::~SimInfo() {
         delete i->second;
     }
     molecules_.clear();
-    
-    MemoryUtils::deletePointers(moleculeStamps_);
-    
+       
+    delete stamps_;
     delete sman_;
     delete simParams_;
     delete forceField_;
@@ -380,19 +379,6 @@ void SimInfo::addExcludePairs(Molecule* mol) {
         }
     }        
 
-    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) {
@@ -450,19 +436,6 @@ void SimInfo::removeExcludePairs(Molecule* mol) {
         }
     }        
 
-    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);
-            }
-        }
-    }  
-
 }
 
 
@@ -697,9 +670,6 @@ 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();
@@ -887,11 +857,10 @@ 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;