--- trunk/src/brains/SimInfo.cpp	2005/01/25 21:59:18	274
+++ trunk/src/brains/SimInfo.cpp	2005/03/11 15:00:20	432
@@ -56,6 +56,7 @@
 #include "UseTheForce/notifyCutoffs_interface.h"
 #include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
+#include "selection/SelectionManager.hpp"
 
 #ifdef IS_MPI
 #include "UseTheForce/mpiComponentPlan.h"
@@ -137,18 +138,21 @@ SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
 #ifdef IS_MPI    
     molToProcMap_.resize(nGlobalMols_);
 #endif
-    
+
 }
 
 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_;
-
 }
 
 int SimInfo::getNGlobalConstraints() {
@@ -363,7 +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) {
@@ -408,6 +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);
+            }
+        }
+    }  
+
 }
 
 
@@ -642,9 +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();
@@ -751,9 +803,7 @@ double SimInfo::calcMaxCutoffRadius() {
     return maxCutoffRadius;
 }
 
-void SimInfo::setupCutoff() {
-    double rcut_;  //cutoff radius
-    double rsw_; //switching radius
+void SimInfo::getCutoff(double& rcut, double& rsw) {
     
     if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
         
@@ -764,9 +814,9 @@ void SimInfo::setupCutoff() {
                 "\tfor the cutoffRadius.\n");
             painCave.isFatal = 0;
             simError();
-            rcut_ = 15.0;
+            rcut = 15.0;
         } else{
-            rcut_ = simParams_->getRcut();
+            rcut = simParams_->getRcut();
         }
 
         if (!simParams_->haveRsw()){
@@ -776,9 +826,9 @@ void SimInfo::setupCutoff() {
                 "\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 {
@@ -786,20 +836,23 @@ void SimInfo::setupCutoff() {
         //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;
         }
     
     }
-        
+}
+
+void SimInfo::setupCutoff() {
+    getCutoff(rcut_, rsw_);    
     double rnblist = rcut_ + 1; // skin of neighbor list
 
     //Pass these cutoff radius etc. to fortran. This function should be called once and only once
@@ -831,6 +884,10 @@ void SimInfo::setSnapshotManager(SnapshotManager* sman
 }
 
 void SimInfo::setSnapshotManager(SnapshotManager* sman) {
+    if (sman_ == sman) {
+        return;
+    }    
+    delete sman_;
     sman_ = sman;
 
     Molecule* mol;