--- trunk/src/brains/Stats.cpp	2009/03/13 20:26:32	1328
+++ trunk/src/brains/Stats.cpp	2011/09/23 20:52:24	1638
@@ -1,24 +1,15 @@
 /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ * Copyright (c) 2005, 2009 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
+ * 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).                        
  */
   
 /**
@@ -49,7 +49,7 @@
 
 #include "brains/Stats.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   bool Stats::isInit_ = false;
   std::string Stats::title_[Stats::ENDINDEX - Stats::BEGININDEX];
@@ -88,6 +88,7 @@ namespace oopse {
     Stats::title_[INVERSION_POTENTIAL] = "Inversion Potential";
     Stats::title_[VRAW] = "Raw Potential";
     Stats::title_[VHARM] = "Harmonic Potential";
+    Stats::title_[SHADOWH] = "Shadow Hamiltonian";
     Stats::title_[PRESSURE_TENSOR_XX] = "P_xx";
     Stats::title_[PRESSURE_TENSOR_XY] = "P_xy";
     Stats::title_[PRESSURE_TENSOR_XZ] = "P_xz";
@@ -101,6 +102,10 @@ namespace oopse {
     Stats::title_[BOX_DIPOLE_Y] = "box dipole y";
     Stats::title_[BOX_DIPOLE_Z] = "box dipole z";
     Stats::title_[TAGGED_PAIR_DISTANCE] = "Tagged_Pair_Distance";
+    Stats::title_[RNEMD_EXCHANGE_TOTAL] = "RNEMD_exchange_total";
+    Stats::title_[THERMAL_HELFANDMOMENT_X] = "Thermal Helfand Moment x";
+    Stats::title_[THERMAL_HELFANDMOMENT_Y] = "Thermal Helfand Moment y";
+    Stats::title_[THERMAL_HELFANDMOMENT_Z] = "Thermal Helfand Moment z";
     
     Stats::units_[TIME] = "fs";
     Stats::units_[TOTAL_ENERGY] = "kcal/mol";
@@ -124,6 +129,7 @@ namespace oopse {
     Stats::units_[INVERSION_POTENTIAL] = "kcal/mol";
     Stats::units_[VRAW] = "kcal/mol";
     Stats::units_[VHARM] = "kcal/mol";
+    Stats::units_[SHADOWH] = "kcal/mol";
     Stats::units_[PRESSURE_TENSOR_XX] = "amu*fs^-2*Ang^-1";
     Stats::units_[PRESSURE_TENSOR_XY] = "amu*fs^-2*Ang^-1";
     Stats::units_[PRESSURE_TENSOR_XZ] = "amu*fs^-2*Ang^-1";
@@ -137,7 +143,10 @@ namespace oopse {
     Stats::units_[BOX_DIPOLE_Y] = "C*m";
     Stats::units_[BOX_DIPOLE_Z] = "C*m";
     Stats::units_[TAGGED_PAIR_DISTANCE] = "Ang";
-    Stats::units_[RNEMD_SWAP_TOTAL] = "Variable";
+    Stats::units_[RNEMD_EXCHANGE_TOTAL] = "Variable";
+    Stats::units_[THERMAL_HELFANDMOMENT_X] = "Ang*kcal/mol";
+    Stats::units_[THERMAL_HELFANDMOMENT_Y] = "Ang*kcal/mol";
+    Stats::units_[THERMAL_HELFANDMOMENT_Z] = "Ang*kcal/mol";
 
     Stats::statsMap.insert(StatsMapType::value_type("TIME", TIME));
     Stats::statsMap.insert(StatsMapType::value_type("TOTAL_ENERGY", TOTAL_ENERGY));
@@ -174,7 +183,11 @@ namespace oopse {
     Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Y", BOX_DIPOLE_Y));    
     Stats::statsMap.insert(StatsMapType::value_type("BOX_DIPOLE_Z", BOX_DIPOLE_Z));    
     Stats::statsMap.insert(StatsMapType::value_type("TAGGED_PAIR_DISTANCE", TAGGED_PAIR_DISTANCE));    
-    Stats::statsMap.insert(StatsMapType::value_type("RNEMD_SWAP_TOTAL", RNEMD_SWAP_TOTAL));    
+    Stats::statsMap.insert(StatsMapType::value_type("RNEMD_EXCHANGE_TOTAL", RNEMD_EXCHANGE_TOTAL));    
+    Stats::statsMap.insert(StatsMapType::value_type("SHADOWH", SHADOWH));
+    Stats::statsMap.insert(StatsMapType::value_type("THERMAL_HELFANDMOMENT_X",THERMAL_HELFANDMOMENT_X));
+    Stats::statsMap.insert(StatsMapType::value_type("THERMAL_HELFANDMOMENT_Y",THERMAL_HELFANDMOMENT_Y));
+    Stats::statsMap.insert(StatsMapType::value_type("THERMAL_HELFANDMOMENT_Z",THERMAL_HELFANDMOMENT_Z));
   }
 
 }