--- trunk/OOPSE/libmdtools/Integrator.cpp	2004/05/01 18:52:38	1144
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2004/05/20 20:24:07	1180
@@ -32,7 +32,7 @@ template<typename T> Integrator<T>::Integrator(SimInfo
 
   nAtoms = info->n_atoms;
   integrableObjects = info->integrableObjects;
-
+ 
   // check for constraints
 
   constrainedA = NULL;
@@ -45,6 +45,9 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   nConstrained = 0;
 
   checkConstraints();
+
+  for (i=0; i<nMols; i++)
+    zAngle[i] = 0.0;
 }
 
 template<typename T> Integrator<T>::~Integrator(){
@@ -160,7 +163,7 @@ template<typename T> void Integrator<T>::integrate(voi
   double thermalTime = info->thermalTime;
   double resetTime = info->resetTime;
 
-
+  double difference;
   double currSample;
   double currThermal;
   double currStatus;
@@ -183,6 +186,11 @@ template<typename T> void Integrator<T>::integrate(voi
   // that was drifting
   tStats->removeCOMdrift();
 
+  // initialize the retraints if necessary
+  if (info->useThermInt) {
+    myFF->initRestraints();
+  }
+
   // initialize the forces before the first step
 
   calcForce(1, 1);
@@ -215,7 +223,8 @@ template<typename T> void Integrator<T>::integrate(voi
 #endif // is_mpi
 
   while (info->getTime() < runTime && !stopIntegrator()){
-    if ((info->getTime() + dt) >= currStatus){
+    difference = info->getTime() + dt - currStatus;
+    if (difference > 0 || fabs(difference) < 1e-4 ){
       calcPot = 1;
       calcStress = 1;
     }
@@ -248,6 +257,7 @@ template<typename T> void Integrator<T>::integrate(voi
 
     if (info->getTime() >= currStatus){
       statOut->writeStat(info->getTime());
+      statOut->writeRaw(info->getTime());
       calcPot = 0;
       calcStress = 0;
       currStatus += statusTime;
@@ -270,6 +280,11 @@ template<typename T> void Integrator<T>::integrate(voi
 #endif // is_mpi
   }
 
+  // dump out a file containing the omega values for the final configuration
+  if (info->useThermInt)
+    myFF->dumpzAngle();
+  
+
   delete dumpOut;
   delete statOut;
 }
@@ -346,8 +361,6 @@ template<typename T> void Integrator<T>::moveA(void){
     integrableObjects[i]->getVel(vel);
     integrableObjects[i]->getPos(pos);
     integrableObjects[i]->getFrc(frc);
-
-    std::cerr << "i =\t" << i << "\t" << frc[0] << "\t" << frc[1]<< "\t" << frc[2] << "\n";
     
     mass = integrableObjects[i]->getMass();