--- trunk/src/brains/Thermo.cpp	2008/09/12 20:51:22	1292
+++ branches/development/src/brains/Thermo.cpp	2010/07/09 23:08:25	1465
@@ -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 <math.h>
@@ -49,9 +49,9 @@
 #include "brains/Thermo.hpp"
 #include "primitives/Molecule.hpp"
 #include "utils/simError.h"
-#include "utils/OOPSEConstant.hpp"
+#include "utils/PhysicalConstants.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   RealType Thermo::getKinetic() {
     SimInfo::MoleculeIterator miter;
@@ -103,7 +103,7 @@ namespace oopse {
 
 #endif //is_mpi
 
-    kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
+    kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
 
     return kinetic;
   }
@@ -139,7 +139,7 @@ namespace oopse {
 
   RealType Thermo::getTemperature() {
     
-    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
+    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
     return temperature;
   }
 
@@ -158,7 +158,7 @@ namespace oopse {
 
     tensor = getPressureTensor();
 
-    pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
+    pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
 
     return pressure;
   }
@@ -173,7 +173,7 @@ namespace oopse {
 
     tensor = getPressureTensor();
 
-    pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
+    pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
 
     return pressure;
   }
@@ -210,7 +210,7 @@ namespace oopse {
     Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
     Mat3x3d tau = curSnapshot->statData.getTau();
 
-    pressureTensor =  (p_global + OOPSEConstant::energyConvert* tau)/volume;
+    pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
     
     return pressureTensor;
   }
@@ -249,16 +249,21 @@ namespace oopse {
         Vector3d pos1, pos2, rab;
 
 #ifdef IS_MPI        
+        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
 
 	int mol1 = info_->getGlobalMolMembership(tap.first);
 	int mol2 = info_->getGlobalMolMembership(tap.second);
-        
+        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
+
         int proc1 = info_->getMolToProc(mol1);
         int proc2 = info_->getMolToProc(mol2);
 
+        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
+
 	RealType data[3];
         if (proc1 == worldRank) {
           StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
+          std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
           pos1 = sd1->getPos();
           data[0] = pos1.x();
           data[1] = pos1.y();
@@ -272,6 +277,7 @@ namespace oopse {
 
         if (proc2 == worldRank) {
           StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
+          std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
           pos2 = sd2->getPos();
           data[0] = pos2.x();
           data[1] = pos2.y();
@@ -298,4 +304,4 @@ namespace oopse {
     
   }
 
-} //end namespace oopse
+} //end namespace OpenMD