--- trunk/src/primitives/Molecule.cpp	2008/01/23 16:38:22	1211
+++ trunk/src/primitives/Molecule.cpp	2009/11/25 20:02:06	1390
@@ -6,19 +6,10 @@
  * 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
+ * 1. 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
+ * 2. 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.
@@ -37,6 +28,15 @@
  * 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.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 /**
@@ -53,7 +53,7 @@
 #include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
   Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) 
     : stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
   }
@@ -64,6 +64,7 @@ namespace oopse {
     MemoryUtils::deletePointers(bonds_);
     MemoryUtils::deletePointers(bends_);
     MemoryUtils::deletePointers(torsions_);
+    MemoryUtils::deletePointers(inversions_);
     MemoryUtils::deletePointers(rigidBodies_);
     MemoryUtils::deletePointers(cutoffGroups_);
     MemoryUtils::deletePointers(constraintPairs_);
@@ -97,6 +98,13 @@ namespace oopse {
       torsions_.push_back(torsion);
     }
   }
+
+  void Molecule::addInversion(Inversion* inversion) {
+    if (std::find(inversions_.begin(), inversions_.end(), inversion) == 
+        inversions_.end()) {
+      inversions_.push_back(inversion);
+    }
+  }
   
   void Molecule::addRigidBody(RigidBody *rb) {
     if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == 
@@ -237,9 +245,11 @@ namespace oopse {
     Bond* bond;
     Bend* bend;
     Torsion* torsion;
+    Inversion* inversion;
     Molecule::BondIterator bondIter;;
     Molecule::BendIterator  bendIter;
     Molecule::TorsionIterator  torsionIter;
+    Molecule::InversionIterator  inversionIter;
 
     RealType potential = 0.0;
 
@@ -256,10 +266,42 @@ namespace oopse {
       potential += torsion->getPotential();
     }
     
+    for (inversion = beginInversion(inversionIter); torsion != NULL; 
+         inversion =  nextInversion(inversionIter)) {
+      potential += inversion->getPotential();
+    }
+    
     return potential;
     
   }
   
+  void Molecule::addProperty(GenericData* genData) {
+    properties_.addProperty(genData);  
+  }
+
+  void Molecule::removeProperty(const std::string& propName) {
+    properties_.removeProperty(propName);  
+  }
+
+  void Molecule::clearProperties() {
+    properties_.clearProperties(); 
+  }
+
+  std::vector<std::string> Molecule::getPropertyNames() {
+    return properties_.getPropertyNames();  
+  }
+      
+  std::vector<GenericData*> Molecule::getProperties() { 
+    return properties_.getProperties(); 
+  }
+
+  GenericData* Molecule::getPropertyByName(const std::string& propName) {
+    return properties_.getPropertyByName(propName); 
+  }
+
+
+
+
   std::ostream& operator <<(std::ostream& o, Molecule& mol) {
     o << std::endl;
     o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
@@ -267,6 +309,7 @@ namespace oopse {
     o << mol.getNBonds() << " bonds" << std::endl;
     o << mol.getNBends() << " bends" << std::endl;
     o << mol.getNTorsions() << " torsions" << std::endl;
+    o << mol.getNInversions() << " inversions" << std::endl;
     o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
     o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
     o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
@@ -274,4 +317,4 @@ namespace oopse {
     return o;
   }
   
-}//end namespace oopse
+}//end namespace OpenMD