--- trunk/OOPSE/libmdtools/Integrator.cpp	2004/04/15 16:18:26	1113
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2004/05/27 20:06:38	1207
@@ -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 +45,7 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   nConstrained = 0;
 
   checkConstraints();
+
 }
 
 template<typename T> Integrator<T>::~Integrator(){
@@ -160,7 +161,7 @@ template<typename T> void Integrator<T>::integrate(voi
   double thermalTime = info->thermalTime;
   double resetTime = info->resetTime;
 
-
+  double difference;
   double currSample;
   double currThermal;
   double currStatus;
@@ -178,6 +179,15 @@ template<typename T> void Integrator<T>::integrate(voi
   dt2 = 0.5 * dt;
 
   readyCheck();
+
+  // remove center of mass drift velocity (in case we passed in a configuration
+  // that was drifting
+  tStats->removeCOMdrift();
+
+  // initialize the retraints if necessary
+  if (info->useThermInt) {
+    myFF->initRestraints();
+  }
 
   // initialize the forces before the first step
 
@@ -211,7 +221,8 @@ 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;
     }
@@ -244,6 +255,8 @@ template<typename T> void Integrator<T>::integrate(voi
 
     if (info->getTime() >= currStatus){
       statOut->writeStat(info->getTime());
+      if (info->useThermInt)
+	statOut->writeRaw(info->getTime());
       calcPot = 0;
       calcStress = 0;
       currStatus += statusTime;
@@ -265,6 +278,11 @@ template<typename T> void Integrator<T>::integrate(voi
     MPIcheckPoint();
 #endif // is_mpi
   }
+
+  // dump out a file containing the omega values for the final configuration
+  if (info->useThermInt)
+    myFF->dumpzAngle();
+  
 
   delete dumpOut;
   delete statOut;
@@ -300,9 +318,7 @@ template<typename T> void Integrator<T>::integrateStep
   MPIcheckPoint();
 #endif // is_mpi
 
-
   // calc forces
-
   calcForce(calcPot, calcStress);
 
 #ifdef IS_MPI
@@ -337,6 +353,7 @@ template<typename T> void Integrator<T>::moveA(void){
   double Tb[3], ji[3];
   double vel[3], pos[3], frc[3];
   double mass;
+  double omega;
  
   for (i = 0; i < integrableObjects.size() ; i++){
     integrableObjects[i]->getVel(vel);
@@ -687,6 +704,7 @@ template<typename T> void Integrator<T>::rotationPropa
 
   double angle;
   double A[3][3], I[3][3];
+  int i, j, k;
 
   // use the angular velocities to propagate the rotation matrix a
   // full time step
@@ -694,26 +712,43 @@ template<typename T> void Integrator<T>::rotationPropa
   sd->getA(A);
   sd->getI(I);
 
-  // rotate about the x-axis
-  angle = dt2 * ji[0] / I[0][0];
-  this->rotate( 1, 2, angle, ji, A );
+  if (sd->isLinear()) {
+    i = sd->linearAxis();
+    j = (i+1)%3;
+    k = (i+2)%3;
+    
+    angle = dt2 * ji[j] / I[j][j];
+    this->rotate( k, i, angle, ji, A );
 
-  // rotate about the y-axis
-  angle = dt2 * ji[1] / I[1][1];
-  this->rotate( 2, 0, angle, ji, A );
+    angle = dt * ji[k] / I[k][k];
+    this->rotate( i, j, angle, ji, A);
 
-  // rotate about the z-axis
-  angle = dt * ji[2] / I[2][2];
-  this->rotate( 0, 1, angle, ji, A);
+    angle = dt2 * ji[j] / I[j][j];
+    this->rotate( k, i, angle, ji, A );
 
-  // rotate about the y-axis
-  angle = dt2 * ji[1] / I[1][1];
-  this->rotate( 2, 0, angle, ji, A );
-
-  // rotate about the x-axis
-  angle = dt2 * ji[0] / I[0][0];
-  this->rotate( 1, 2, angle, ji, A );
-
+  } else {
+    // rotate about the x-axis
+    angle = dt2 * ji[0] / I[0][0];
+    this->rotate( 1, 2, angle, ji, A );
+    
+    // rotate about the y-axis
+    angle = dt2 * ji[1] / I[1][1];
+    this->rotate( 2, 0, angle, ji, A );
+    
+    // rotate about the z-axis
+    angle = dt * ji[2] / I[2][2];
+    sd->addZangle(angle);
+    this->rotate( 0, 1, angle, ji, A);
+    
+    // rotate about the y-axis
+    angle = dt2 * ji[1] / I[1][1];
+    this->rotate( 2, 0, angle, ji, A );
+    
+    // rotate about the x-axis
+    angle = dt2 * ji[0] / I[0][0];
+    this->rotate( 1, 2, angle, ji, A );
+    
+  }
   sd->setA( A  );
 }