--- trunk/src/io/Globals.cpp	2009/10/19 13:35:42	1367
+++ trunk/src/io/Globals.cpp	2009/12/08 22:17:02	1398
@@ -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 <stdlib.h>
@@ -49,7 +49,7 @@
 #include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
 Globals::Globals() {
   DefineParameter(ForceField, "forceField")
  
@@ -99,8 +99,6 @@ Globals::Globals() {
   DefineOptionalParameter(BeadSize, "beadSize");
   DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
   DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
-  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
-  DefineOptionalParameter(ThermalLength, "thermalLength");
   DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
   DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
   DefineOptionalParameter(MTM_Ce, "MTM_Ce");
@@ -199,8 +197,6 @@ void Globals::validate() {
   CheckParameter(DampingAlpha,isNonNegative());
   CheckParameter(SkinThickness, isPositive());
   CheckParameter(Viscosity, isNonNegative());
-  CheckParameter(ThermalConductivity, isNonNegative());
-  CheckParameter(ThermalLength, isNonNegative());
   CheckParameter(BeadSize, isPositive());
   CheckParameter(FrozenBufferRadius, isPositive());
   CheckParameter(LangevinBufferRadius, isPositive());
@@ -214,7 +210,7 @@ void Globals::validate() {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
         std::ostringstream oss;
         oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
-        throw OOPSEException(oss.str());           
+        throw OpenMDException(oss.str());           
     }
   }
 }
@@ -245,7 +241,7 @@ bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
     } else {
         std::ostringstream oss;
         oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
-        throw OOPSEException(oss.str());  
+        throw OpenMDException(oss.str());  
     }
     return ret;
 }