--- trunk/src/primitives/CutoffGroup.hpp	2004/09/24 16:27:58	3
+++ trunk/src/primitives/CutoffGroup.hpp	2005/01/12 22:41:40	246
@@ -1,90 +1,137 @@
-#ifndef _CUTOFFGROUP_H_
-#define _CUTOFFGROUP_H_
+ /*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * non-exclusive, royalty free, license to use, modify and
+ * redistribute this software in source and binary code form, provided
+ * that the following conditions are met:
+ *
+ * 1. Acknowledgement of the program authors must be made in any
+ *    publication of scientific results based in part on use of the
+ *    program.  An acceptable form of acknowledgement is citation of
+ *    the article in which the program was described (Matthew
+ *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
+ *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
+ *    Parallel Simulation Engine for Molecular Dynamics,"
+ *    J. Comput. Chem. 26, pp. 252-271 (2005))
+ *
+ * 2. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 3. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * arising out of the use of or inability to use software, even if the
+ * University of Notre Dame has been advised of the possibility of
+ * such damages.
+ */
+ 
+#ifndef PRIMITIVES_CUTOFFGROUP_HPP
+
+#define PRIMITIVES_CUTOFFGROUP_HPP
+
 #include "primitives/Atom.hpp"
+#include "math/Vector3.hpp"
 
-class CutoffGroup{
-public:
-  
-  CutoffGroup() { 
-    haveTotalMass = false; 
-    totalMass = 0.0;
-  }
-  
-  void addAtom(Atom* atom) {cutoffAtomList.push_back(atom);}
-  
-  Atom* beginAtom(vector<Atom*>::iterator& i){
-    i = cutoffAtomList.begin();
-    return i != cutoffAtomList.end()? *i : NULL;
-  }
-  
-  Atom* nextAtom(vector<Atom*>::iterator& i){
-    i++;
-    return i != cutoffAtomList.end()? *i : NULL;
-  }
-  
-  double getMass(){
-    vector<Atom*>::iterator i;
-    Atom* atom;
-    double mass;
-    
-    if (!haveTotalMass) {
+namespace oopse {
+class CutoffGroup {
+    public:
 
-      totalMass = 0;
-      
-      for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
-        mass = atom->getMass();
-        totalMass += mass;
-      }
+        CutoffGroup() {
+            haveTotalMass = false;
+            totalMass = 0.0;
+        }
 
-      haveTotalMass = true;
-    }
-    
-    return totalMass;
-  }
-  
-  void getCOM(double com[3]){
+        void addAtom(Atom *atom) {
+            cutoffAtomList.push_back(atom);
+        }
 
-    vector<Atom*>::iterator i;
-    Atom* atom;
-    double pos[3];
-    double mass;
-    
-    com[0] = 0;
-    com[1] = 0;
-    com[2] = 0;
-    totalMass = getMass();    
-    
-    if (cutoffAtomList.size() == 1) {
-      
-      beginAtom(i)->getPos(com);
-      
-    } else {
-      
-      for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
-        mass = atom->getMass();
-        atom->getPos(pos);
-        com[0] += pos[0] * mass;
-        com[1] += pos[1] * mass;
-        com[2] += pos[2] * mass;
-      }
-      
-      com[0] /= totalMass;
-      com[1] /= totalMass;
-      com[2] /= totalMass;
-    }
-    
-  }
-  
-  int getNumAtom() {return cutoffAtomList.size();}
+        Atom *beginAtom(std::vector<Atom *>::iterator & i) {
+            i = cutoffAtomList.begin();
+            return i != cutoffAtomList.end() ? *i : NULL;
+        }
 
-  int getGlobalIndex() {return globalIndex;}
-  void setGlobalIndex(int id) {this->globalIndex = id;}
-private:
-  vector<Atom*> cutoffAtomList;
-  bool haveTotalMass;
-  double totalMass;
-  int globalIndex;
+        Atom *nextAtom(std::vector<Atom *>::iterator & i) {
+            i++;
+            return i != cutoffAtomList.end() ? *i : NULL;
+        }
 
+        double getMass() {
+            std::vector<Atom *>::iterator i;
+            Atom * atom;
+            double mass;
+
+            if (!haveTotalMass) {
+                totalMass = 0;
+
+                for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
+                    mass = atom->getMass();
+                    totalMass += mass;
+                }
+
+                haveTotalMass = true;
+            }
+
+            return totalMass;
+        }
+
+        void getCOM(Vector3d & com) {
+            std::vector<Atom *>::iterator i;
+            Atom * atom;
+            Vector3d pos;
+            double mass;
+
+            com[0] = 0;
+            com[1] = 0;
+            com[2] = 0;
+            totalMass = getMass();
+
+            if (cutoffAtomList.size() == 1) {
+                com = beginAtom(i)->getPos();
+            } else {
+                for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
+                    mass = atom->getMass();
+                    pos = atom->getPos();
+                    com += pos * mass;
+                }
+
+                com /= totalMass;
+            }
+        }
+
+        int getNumAtom() {
+            return cutoffAtomList.size();
+        }
+
+        int getGlobalIndex() {
+            return globalIndex;
+        }
+
+        void setGlobalIndex(int id) {
+            this->globalIndex = id;
+        }
+
+    private:
+
+        std::vector<Atom *>cutoffAtomList;
+        bool haveTotalMass;
+        double totalMass;
+        int globalIndex;
 };
 
-#endif
+}      //end namespace oopse
+
+#endif //PRIMITIVES_CUTOFFGROUP_HPP