--- branches/new_design/OOPSE-4/src/primitives/Molecule.cpp	2004/12/03 20:30:07	1842
+++ branches/new_design/OOPSE-4/src/primitives/Molecule.cpp	2004/12/03 21:30:30	1843
@@ -96,9 +96,6 @@ void Molecule::complete() {
 
 void Molecule::complete() {
     
-    std::set<Atom*> allAtoms;
-    allAtoms.insert(atoms_.begin(), atoms_.end());
-
     std::set<Atom*> rigidAtoms;
     RigidBody* rb;
     std::vector<RigidBody*>::iterator rbIter;
@@ -108,21 +105,29 @@ void Molecule::complete() {
         rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
     }
 
+    Atom* atom;
+    AtomIterator ai;
+    for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) {
+        if (rigidAtoms.find(*ai) != rigidAtoms.end()) {
+            integrableObjects_.push_back(*ai);
+        }
+    }
+
     //find all free atoms (which do not belong to rigid bodies)  
     //performs the "difference" operation from set theory,  the output range contains a copy of every
     //element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in 
     //[rigidAtoms.begin(), rigidAtoms.end()).
-    std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
-                            std::back_inserter(integrableObjects_));
+    //std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
+    //                        std::back_inserter(integrableObjects_));
 
-    if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
-        //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
-        sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
+    //if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
+    //    //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
+    //    sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
+    //
+    //    painCave.isFatal = 1;
+    //    simError();        
+    //}
 
-        painCave.isFatal = 1;
-        simError();        
-    }
-
     integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
 }
 
@@ -197,8 +202,20 @@ CutoffGroup* Molecule::nextCutoffGroup(std::vector<Cut
     ++i;
     return (i == cutoffGroups_.end()) ? NULL : *i;    
 } 
+
+double Molecule::getMass() {
+    StuntDouble* sd;
+    std::vector<StuntDouble*>::iterator i;
+    double mass = 0.0;
+
+    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
+        mass += sd->getMass();
+    }
 
+    return mass;
 
+}
+
 Vector3d Molecule::getCom() {
     StuntDouble* sd;
     std::vector<StuntDouble*>::iterator i;
@@ -245,6 +262,33 @@ std::ostream& operator <<(std::ostream& o, Molecule& m
     return velCom;
 }
 
+double Molecule::getPotential() {
+
+    Bond* bond;
+    Bend* bend;
+    Torsion* torsion;
+    Molecule::BondIterator bondIter;;
+    Molecule::BendIterator  bendIter;
+    Molecule::TorsionIterator  torsionIter;
+
+    double potential = 0.0;
+
+    for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
+        potential += bond->getPotential();
+    }
+
+    for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
+        potential += bend->getPotential();
+    }
+
+    for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
+        potential += torsion->getPotential();
+    }
+
+    return potential;
+
+}
+
 std::ostream& operator <<(std::ostream& o, Molecule& mol) {
     o << std::endl;
     o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;