--- trunk/src/integrators/RNEMD.cpp	2009/10/19 13:39:04	1368
+++ trunk/src/integrators/RNEMD.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).                        
  */
 
 #include <cmath>
@@ -46,7 +46,7 @@
 #include "math/Polynomial.hpp"
 #include "primitives/Molecule.hpp"
 #include "primitives/StuntDouble.hpp"
-#include "utils/OOPSEConstant.hpp"
+#include "utils/PhysicalConstants.hpp"
 #include "utils/Tuple.hpp"
 
 #ifndef IS_MPI
@@ -57,7 +57,7 @@
 
 #define HONKING_LARGE_VALUE 1.0e10
 
-namespace oopse {
+namespace OpenMD {
   
   RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
 
@@ -279,7 +279,7 @@ namespace oopse {
           }
           //make exchangeSum_ comparable between swap & scale
           //temporarily without using energyConvert
-          //value = value * 0.5 / OOPSEConstant::energyConvert;
+          //value = value * 0.5 / PhysicalConstants::energyConvert;
           value *= 0.5;
           break;
         case rnemdPx :
@@ -915,19 +915,19 @@ namespace oopse {
             valueCount_[binNo] +=3;
 	  }
 	}
-	value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
+	value = value / PhysicalConstants::energyConvert / PhysicalConstants::kb;
 
 	break;
       case rnemdPx :
       case rnemdPxScale :
 	value = mass * vel[0];
         valueCount_[binNo]++;
-        xVal = mass * vel.x() * vel.x() / OOPSEConstant::energyConvert
-          / OOPSEConstant::kb;
-        yVal = mass * vel.y() * vel.y() / OOPSEConstant::energyConvert
-          / OOPSEConstant::kb;
-        zVal = mass * vel.z() * vel.z() / OOPSEConstant::energyConvert
-          / OOPSEConstant::kb;
+        xVal = mass * vel.x() * vel.x() / PhysicalConstants::energyConvert
+          / PhysicalConstants::kb;
+        yVal = mass * vel.y() * vel.y() / PhysicalConstants::energyConvert
+          / PhysicalConstants::kb;
+        zVal = mass * vel.z() * vel.z() / PhysicalConstants::energyConvert
+          / PhysicalConstants::kb;
         xTempHist_[binNo] += xVal;
         yTempHist_[binNo] += yVal;
         zTempHist_[binNo] += zVal;
@@ -1010,8 +1010,10 @@ namespace oopse {
       }
       for (j = 0; j < rnemdLogWidth_; j++) valueCount_[j] = 0;
 #ifdef IS_MPI
-    }
+    }    
 #endif
+
+      
   }
 
 }