--- trunk/src/integrators/NPTi.cpp	2006/05/17 21:51:42	963
+++ trunk/src/integrators/NPTi.cpp	2010/05/10 17:28:26	1442
@@ -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 "NPTi.hpp"
@@ -44,10 +44,10 @@
 #include "brains/Thermo.hpp"
 #include "integrators/NPT.hpp"
 #include "primitives/Molecule.hpp"
-#include "utils/OOPSEConstant.hpp"
+#include "utils/PhysicalConstants.hpp"
 #include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
 
   // Basic isotropic thermostating and barostating via the Melchionna
   // modification of the Hoover algorithm:
@@ -65,7 +65,7 @@ namespace oopse {
 
   void NPTi::evolveEtaA() {
     eta += dt2 * ( instaVol * (instaPress - targetPressure) /
-		   (OOPSEConstant::pressureConvert*NkBT*tb2));
+		   (PhysicalConstants::pressureConvert*NkBT*tb2));
     oldEta = eta;
   }
 
@@ -73,7 +73,7 @@ namespace oopse {
 
     prevEta = eta;
     eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
-			   (OOPSEConstant::pressureConvert*NkBT*tb2));
+			   (PhysicalConstants::pressureConvert*NkBT*tb2));
   }
 
   void NPTi::calcVelScale() {
@@ -131,12 +131,12 @@ namespace oopse {
     // We need NkBT a lot, so just set it here: This is the RAW number
     // of integrableObjects, so no subtraction or addition of constraints or
     // orientational degrees of freedom:
-    NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp;
+    NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp;
 
     // fkBT is used because the thermostat operates on more degrees of freedom
     // than the barostat (when there are particles with orientational degrees
     // of freedom).  
-    fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp;    
+    fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp;    
     
     RealType conservedQuantity;
     RealType Energy;
@@ -147,15 +147,15 @@ namespace oopse {
 
     Energy =thermo.getTotalE();
 
-    thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * OOPSEConstant::energyConvert);
+    thermostat_kinetic = fkBT* tt2 * chi * chi / (2.0 * PhysicalConstants::energyConvert);
 
-    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
+    thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
 
 
-    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * OOPSEConstant::energyConvert);
+    barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /(2.0 * PhysicalConstants::energyConvert);
 
-    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /
-      OOPSEConstant::energyConvert;
+    barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /
+      PhysicalConstants::energyConvert;
 
     conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
       barostat_kinetic + barostat_potential;
@@ -166,7 +166,7 @@ namespace oopse {
   void NPTi::loadEta() {
     Mat3x3d etaMat = currentSnapshot_->getEta();
     eta = etaMat(0,0);
-    //if (fabs(etaMat(1,1) - eta) >= oopse::epsilon || fabs(etaMat(1,1) - eta) >= oopse::epsilon || !etaMat.isDiagonal()) {
+    //if (fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || fabs(etaMat(1,1) - eta) >= OpenMD::epsilon || !etaMat.isDiagonal()) {
     //    sprintf( painCave.errMsg,
     //             "NPTi error: the diagonal elements of  eta matrix are not the same or etaMat is not a diagonal matrix");
     //    painCave.isFatal = 1;