--- trunk/src/integrators/NPTxyz.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/integrators/NPTxyz.cpp	2013/06/16 15:15:42	1879
@@ -35,8 +35,9 @@
  *                                                                      
  * [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).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include "brains/SimInfo.hpp"
@@ -61,6 +62,8 @@ namespace OpenMD {
 
     
   RealType NPTxyz::calcConservedQuantity(){
+    thermostat = snap->getThermostat();
+    loadEta();
 
     // 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
@@ -80,11 +83,13 @@ namespace OpenMD {
     RealType barostat_potential;
     RealType trEta;
 
-    totalEnergy = thermo.getTotalE();
+    totalEnergy = thermo.getTotalEnergy();
 
-    thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * PhysicalConstants::energyConvert);
+    thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first 
+      / (2.0 * PhysicalConstants::energyConvert);
 
-    thermostat_potential = fkBT* integralOfChidt / PhysicalConstants::energyConvert;
+    thermostat_potential = fkBT* thermostat.second 
+      / PhysicalConstants::energyConvert;
 
     SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
     trEta = tmp.trace();
@@ -104,15 +109,13 @@ namespace OpenMD {
     
   void NPTxyz::scaleSimBox(){
 
-    int i,j,k;
+    int i, j;
     Mat3x3d scaleMat;
-    RealType eta2ij, scaleFactor;
-    RealType bigScale, smallScale, offDiagMax;
+    RealType scaleFactor;
+    RealType bigScale, smallScale;
     Mat3x3d hm;
     Mat3x3d hmnew;
 
-
-
     // Scale the box after all the positions have been moved:
 
     // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
@@ -120,7 +123,6 @@ namespace OpenMD {
 
     bigScale = 1.0;
     smallScale = 1.0;
-    offDiagMax = 0.0;
 
     for(i=0; i<3; i++){
       for(j=0; j<3; j++){
@@ -162,14 +164,14 @@ namespace OpenMD {
       simError();
     } else {
 
-      Mat3x3d hmat = currentSnapshot_->getHmat();
+      Mat3x3d hmat = snap->getHmat();
       hmat = hmat *scaleMat;
-      currentSnapshot_->setHmat(hmat);
+      snap->setHmat(hmat);
     }
   }
 
   void NPTxyz::loadEta() {
-    eta= currentSnapshot_->getEta();
+    eta= snap->getBarostat();
   }
 
 }