--- branches/development/src/flucq/FluctuatingChargeNVT.cpp	2012/06/05 17:58:55	1739
+++ trunk/src/flucq/FluctuatingChargeNVT.cpp	2015/03/07 21:41:51	2071
@@ -35,7 +35,7 @@
  *                                                                      
  * [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).          
+ * [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).
  */
@@ -45,14 +45,17 @@
 #include "utils/simError.h"
 #include "utils/PhysicalConstants.hpp"
 
+
 namespace OpenMD {
 
-  FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info, ForceManager* fm) : 
-    FluctuatingChargePropagator(info, fm), chiTolerance_ (1e-6), 
-    maxIterNum_(4), thermo(info), 
-    currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
-    
-    if (hasFlucQ_) {     
+  FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) : 
+    FluctuatingChargePropagator(info), maxIterNum_(4), chiTolerance_ (1e-6), 
+    snap(info->getSnapshotManager()->getCurrentSnapshot()), thermo(info) {  
+  }
+
+  void FluctuatingChargeNVT::initialize() {
+    FluctuatingChargePropagator::initialize();  
+    if (hasFlucQ_) {
       if (info_->getSimParams()->haveDt()) {
         dt_ = info_->getSimParams()->getDt();
         dt2_ = dt_ * 0.5;
@@ -64,8 +67,7 @@ namespace OpenMD {
       }
       
       if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
-        currentSnapshot_->setChiElectronic(0.0);
-        currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
+        snap->setElectronicThermostat(make_pair(0.0, 0.0));
       }
       
       if (!fqParams_->haveTargetTemp()) {
@@ -90,15 +92,11 @@ namespace OpenMD {
       } else {
         tauThermostat_ = fqParams_->getTauThermostat();
       }
-      updateSizes();
+      updateSizes(); 
     }
   }
 
-  void FluctuatingChargeNVT::initialize() {
-    FluctuatingChargePropagator::initialize();
-  }
 
-
   void FluctuatingChargeNVT::moveA() {
 
     if (!hasFlucQ_) return;
@@ -109,11 +107,11 @@ namespace OpenMD {
     Atom* atom;
     RealType cvel, cpos, cfrc, cmass;
 
-    RealType chi = currentSnapshot_->getChiElectronic();
-    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
+    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
+    RealType chi = thermostat.first;
+    RealType integralOfChidt = thermostat.second;
     RealType instTemp = thermo.getElectronicTemperature();
 
-
     for (mol = info_->beginMolecule(i); mol != NULL; 
          mol = info_->nextMolecule(i)) {
       for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
@@ -122,20 +120,13 @@ namespace OpenMD {
         cvel = atom->getFlucQVel();
         cpos = atom->getFlucQPos();
         cfrc = atom->getFlucQFrc();
-        cmass = atom->getChargeMass();
-        
-	cerr << atom->getType() << "\n";
-	cerr << "Before\n";
-	cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\tcfrc: " << cfrc << "\tcmass: " << cmass << "\n";
-        
+        cmass = atom->getChargeMass();       
+
 	// velocity half step
         cvel += dt2_ * cfrc / cmass - dt2_*chi*cvel;                    
         // position whole step
         cpos += dt_ * cvel;
 	
-	cerr << "After\n";
-	cerr << "cvel: " << cvel << "\tcpos: " << cpos << "\n\n";        
-
         atom->setFlucQVel(cvel);
         atom->setFlucQPos(cpos);
       }
@@ -145,14 +136,10 @@ namespace OpenMD {
       (tauThermostat_ * tauThermostat_);
 
     integralOfChidt += chi * dt2_;
-    cerr << "Move A instTemp: " << instTemp << "\n";
-    currentSnapshot_->setChiElectronic(chi);
-    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
-       
+    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
   }
 
   void FluctuatingChargeNVT::updateSizes() {
-    if (!hasFlucQ_) return;
     oldVel_.resize(info_->getNFluctuatingCharges());
   }
 
@@ -163,10 +150,11 @@ namespace OpenMD {
     Molecule* mol;
     Atom* atom;
     RealType instTemp;
-    RealType chi = currentSnapshot_->getChiElectronic();
+    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
+    RealType chi = thermostat.first;
     RealType oldChi = chi;
     RealType prevChi;
-    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
+    RealType integralOfChidt = thermostat.second;
     int index;
     RealType cfrc, cvel, cmass;
 
@@ -186,7 +174,6 @@ namespace OpenMD {
     for(int k = 0; k < maxIterNum_; k++) {
       index = 0;
       instTemp = thermo.getElectronicTemperature();
-      cerr << "MoveB instTemp: " << instTemp << "\n";
       // evolve chi another half step using the temperature at t + dt/2
       prevChi = chi;
       chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) / 
@@ -198,12 +185,10 @@ namespace OpenMD {
              atom = mol->nextFluctuatingCharge(j)) {
 
           cfrc = atom->getFlucQFrc();
-          cvel =atom->getFlucQVel();
           cmass = atom->getChargeMass();
           
           // velocity half step
           cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_*chi*oldVel_[index];
-          
           atom->setFlucQVel(cvel);      
           ++index;          
         }
@@ -212,20 +197,19 @@ namespace OpenMD {
         break;
     }
     integralOfChidt += dt2_ * chi;
-    currentSnapshot_->setChiElectronic(chi);
-    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
+    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
   }
   
   void FluctuatingChargeNVT::resetPropagator() {
     if (!hasFlucQ_) return;
-    currentSnapshot_->setChiElectronic(0.0);
-    currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
+    snap->setElectronicThermostat(make_pair(0.0, 0.0));
   }
   
   RealType FluctuatingChargeNVT::calcConservedQuantity() {
     if (!hasFlucQ_) return 0.0;
-    RealType chi = currentSnapshot_->getChiElectronic();
-    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
+    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
+    RealType chi = thermostat.first;
+    RealType integralOfChidt = thermostat.second;
     RealType fkBT = info_->getNFluctuatingCharges() * 
       PhysicalConstants::kB *targetTemp_;