--- branches/new_design/OOPSE-4/src/integrators/NVT.cpp	2004/12/03 17:59:45	1841
+++ branches/new_design/OOPSE-4/src/integrators/NVT.cpp	2004/12/09 16:22:42	1871
@@ -43,7 +43,7 @@ void NVT::update() {
     update();
 }
 
-void NVT::update() {
+void NVT::doUpdate() {
     oldVel_.resize(info_->getNIntegrableObjects());
     oldJi_.resize(info_->getNIntegrableObjects());    
 }
@@ -59,9 +59,8 @@ void NVT::moveA() {
     Vector3d pos;
     Vector3d frc;
 
-    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
-    double chi = currSnapshot->getChi();
-    double integralOfChidt = currSnapshot->getIntegralOfChiDt();
+    double chi = currentSnapshot_->getChi();
+    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
     
     // We need the temperature at time = t for the chi update below:
 
@@ -79,7 +78,7 @@ void NVT::moveA() {
 
         // velocity half step  (use chi from previous step here):
         //vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi);
-        vel = dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel;
+        vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel;
         
         // position whole step
         //pos[j] += dt * vel[j];
@@ -90,11 +89,9 @@ void NVT::moveA() {
 
         if (integrableObject->isDirectional()) {
 
-            // get and convert the torque to body frame
+            //convert the torque to body frame
+            Tb = integrableObject->lab2Body(integrableObject->getTrq());
 
-            Tb = integrableObject->getTrq();
-            integrableObject->lab2Body(Tb);
-
             // get the angular momentum, and propagate a half step
 
             ji = integrableObject->getJ();
@@ -118,8 +115,8 @@ void NVT::moveA() {
     chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_);
     integralOfChidt += chi * dt2;
 
-    currSnapshot->setChi(chi);
-    currSnapshot->setIntegralOfChiDt(integralOfChidt);
+    currentSnapshot_->setChi(chi);
+    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
 }
 
 void NVT::moveB() {
@@ -137,11 +134,10 @@ void NVT::moveB() {
     int index;
     // Set things up for the iteration:
 
-    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
-    double chi = currSnapshot->getChi();
+    double chi = currentSnapshot_->getChi();
     double oldChi = chi;
     double  prevChi;
-    double integralOfChidt = currSnapshot->getIntegralOfChiDt();
+    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
 
     index = 0;
     for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
@@ -149,8 +145,10 @@ void NVT::moveB() {
                integrableObject = mol->nextIntegrableObject(j)) {
                 oldVel_[index] = integrableObject->getVel();
                 oldJi_[index] = integrableObject->getJ();                
+
+                ++index;    
         }
-        ++index;               
+           
     }
 
     // do the iteration:
@@ -184,15 +182,17 @@ void NVT::moveB() {
 
                     // get and convert the torque to body frame
 
-                    Tb = integrableObject->getTrq();
-                    integrableObject->lab2Body(Tb);
+                    Tb =  integrableObject->lab2Body(integrableObject->getTrq());
 
                     //for(j = 0; j < 3; j++)
                     //    ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi);
-                    ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index];
+                    ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index];
 
                     integrableObject->setJ(ji);
                 }
+
+
+                ++index;
             }
         }
     
@@ -202,20 +202,19 @@ void NVT::moveB() {
         if (fabs(prevChi - chi) <= chiTolerance_)
             break;
 
-        ++index;
     }
 
     integralOfChidt += dt2 * chi;
 
-    currSnapshot->setChi(chi);
-    currSnapshot->setIntegralOfChiDt(integralOfChidt);
+    currentSnapshot_->setChi(chi);
+    currentSnapshot_->setIntegralOfChiDt(integralOfChidt);
 }
 
 
 double NVT::calcConservedQuantity() {
-    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
-    double chi = currSnapshot->getChi();
-    double integralOfChidt = currSnapshot->getIntegralOfChiDt();
+
+    double chi = currentSnapshot_->getChi();
+    double integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
     double conservedQuantity;
     double fkBT;
     double Energy;