--- trunk/src/brains/SimInfo.cpp	2005/02/13 20:36:24	328
+++ trunk/src/brains/SimInfo.cpp	2005/04/13 18:41:17	490
@@ -65,15 +65,15 @@ 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),
                                 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 +139,19 @@ 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();
+       
+    delete stamps_;
     delete sman_;
     delete simParams_;
     delete forceField_;
-    delete selectMan_;
 }
 
 int SimInfo::getNGlobalConstraints() {
@@ -366,7 +366,19 @@ 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);
+            }
+        }
+    }        
+
 }
 
 void SimInfo::removeExcludePairs(Molecule* mol) {
@@ -410,6 +422,19 @@ void SimInfo::removeExcludePairs(Molecule* mol) {
         exclude_.removePair(b, d);
         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);
+            }
+        }
+    }        
 
 }
 
@@ -645,9 +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();
@@ -835,6 +857,10 @@ void SimInfo::setSnapshotManager(SnapshotManager* sman
 }
 
 void SimInfo::setSnapshotManager(SnapshotManager* sman) {
+    if (sman_ == sman) {
+        return;
+    }    
+    delete sman_;
     sman_ = sman;
 
     Molecule* mol;