--- branches/new_design/OOPSE-2.0/src/brains/SimInfo.cpp	2004/12/03 17:59:45	1841
+++ branches/new_design/OOPSE-2.0/src/brains/SimInfo.cpp	2004/12/06 04:49:53	1856
@@ -109,9 +109,6 @@ SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
     //file plus the number of  rigid bodies defined in meta-data file
     nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
 
-    //initialize globalGroupMembership_, every element of this array will be 0
-    globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0);
-
     nGlobalMols_ = molStampIds_.size();
 
 #ifdef IS_MPI    
@@ -149,6 +146,8 @@ bool SimInfo::addMolecule(Molecule* mol) {
         nCutoffGroups_ += mol->getNCutoffGroups();
         nConstraints_ += mol->getNConstraints();
 
+        addExcludePairs(mol);
+        
         return true;
     } else {
         return false;
@@ -172,6 +171,7 @@ bool SimInfo::removeMolecule(Molecule* mol) {
         nCutoffGroups_ -= mol->getNCutoffGroups();
         nConstraints_ -= mol->getNConstraints();
 
+        removeExcludePairs(mol);
         molecules_.erase(mol->getGlobalIndex());
 
         delete mol;
@@ -605,7 +605,7 @@ void SimInfo::setupFortranSim() {
     //molMembershipArray is filled by SimCreator    
     std::vector<int> molMembershipArray(nGlobalAtoms_);
     for (int i = 0; i < nGlobalAtoms_; i++) {
-        molMembershipArray.push_back(globalMolMembership_[i] + 1);
+        molMembershipArray[i] = globalMolMembership_[i] + 1;
     }
     
     //setup fortran simulation
@@ -820,9 +820,48 @@ std::ostream& operator <<(std::ostream& o, SimInfo& in
     
 }
 
+Vector3d SimInfo::getComVel(){ 
+    SimInfo::MoleculeIterator i;
+    Molecule* mol;
+
+    Vector3d comVel(0.0);
+    double totalMass = 0.0;
+    
+ 
+    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
+        double mass = mol->getMass();
+        totalMass += mass;
+        comVel += mass * mol->getComVel();
+    }  
+
+    comVel /= totalMass;
+
+    return comVel;
+}
+
+Vector3d SimInfo::getCom(){ 
+    SimInfo::MoleculeIterator i;
+    Molecule* mol;
+
+    Vector3d com(0.0);
+    double totalMass = 0.0;
+     
+    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
+        double mass = mol->getMass();
+        totalMass += mass;
+        com += mass * mol->getCom();
+    }  
+
+    com /= totalMass;
+
+    return com;
+
+}        
+
 std::ostream& operator <<(std::ostream& o, SimInfo& info) {
 
     return o;
 }
 
 }//end namespace oopse
+