--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/12/22 21:27:04	892
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2004/06/02 14:56:18	1221
@@ -31,7 +31,8 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   }
 
   nAtoms = info->n_atoms;
-
+  integrableObjects = info->integrableObjects;
+ 
   // check for constraints
 
   constrainedA = NULL;
@@ -44,6 +45,7 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   nConstrained = 0;
 
   checkConstraints();
+
 }
 
 template<typename T> Integrator<T>::~Integrator(){
@@ -68,7 +70,8 @@ template<typename T> void Integrator<T>::checkConstrai
 
   SRI** theArray;
   for (int i = 0; i < nMols; i++){
-    theArray = (SRI * *) molecules[i].getMyBonds();
+
+	  theArray = (SRI * *) molecules[i].getMyBonds();
     for (int j = 0; j < molecules[i].getNBonds(); j++){
       constrained = theArray[j]->is_constrained();
 
@@ -114,6 +117,7 @@ template<typename T> void Integrator<T>::checkConstrai
     }
   }
 
+
   if (nConstrained > 0){
     isConstrained = 1;
 
@@ -135,7 +139,7 @@ template<typename T> void Integrator<T>::checkConstrai
     }
 
 
-    // save oldAtoms to check for lode balanceing later on.
+    // save oldAtoms to check for lode balancing later on.
 
     oldAtoms = nAtoms;
 
@@ -157,7 +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;
@@ -176,10 +180,19 @@ template<typename T> void Integrator<T>::integrate(voi
 
   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->useSolidThermInt && !info->useLiquidThermInt) {
+    myFF->initRestraints();
+  }
+
   // initialize the forces before the first step
 
   calcForce(1, 1);
-
+  
   if (nConstrained){
     preMove();
     constrainA();
@@ -207,8 +220,9 @@ template<typename T> void Integrator<T>::integrate(voi
   MPIcheckPoint();
 #endif // is_mpi
 
-  while (info->getTime() < runTime){
-    if ((info->getTime() + dt) >= currStatus){
+  while (info->getTime() < runTime && !stopIntegrator()){
+    difference = info->getTime() + dt - currStatus;
+    if (difference > 0 || fabs(difference) < 1e-4 ){
       calcPot = 1;
       calcStress = 1;
     }
@@ -263,10 +277,11 @@ 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->useSolidThermInt && !info->useLiquidThermInt)
+    myFF->dumpzAngle();
+  
 
-  // write the last frame
-  dumpOut->writeDump(info->getTime());
-
   delete dumpOut;
   delete statOut;
 }
@@ -301,9 +316,7 @@ template<typename T> void Integrator<T>::integrateStep
   MPIcheckPoint();
 #endif // is_mpi
 
-
   // calc forces
-
   calcForce(calcPot, calcStress);
 
 #ifdef IS_MPI
@@ -333,19 +346,20 @@ template<typename T> void Integrator<T>::moveA(void){
 
 
 template<typename T> void Integrator<T>::moveA(void){
-  int i, j;
+  size_t i, j;
   DirectionalAtom* dAtom;
   double Tb[3], ji[3];
   double vel[3], pos[3], frc[3];
   double mass;
-
-  for (i = 0; i < nAtoms; i++){
-    atoms[i]->getVel(vel);
-    atoms[i]->getPos(pos);
-    atoms[i]->getFrc(frc);
+  double omega;
+ 
+  for (i = 0; i < integrableObjects.size() ; i++){
+    integrableObjects[i]->getVel(vel);
+    integrableObjects[i]->getPos(pos);
+    integrableObjects[i]->getFrc(frc);
+    
+    mass = integrableObjects[i]->getMass();
 
-    mass = atoms[i]->getMass();
-
     for (j = 0; j < 3; j++){
       // velocity half step
       vel[j] += (dt2 * frc[j] / mass) * eConvert;
@@ -353,27 +367,26 @@ template<typename T> void Integrator<T>::moveA(void){
       pos[j] += dt * vel[j];
     }
 
-    atoms[i]->setVel(vel);
-    atoms[i]->setPos(pos);
+    integrableObjects[i]->setVel(vel);
+    integrableObjects[i]->setPos(pos);
 
-    if (atoms[i]->isDirectional()){
-      dAtom = (DirectionalAtom *) atoms[i];
+    if (integrableObjects[i]->isDirectional()){
 
       // get and convert the torque to body frame
 
-      dAtom->getTrq(Tb);
-      dAtom->lab2Body(Tb);
+      integrableObjects[i]->getTrq(Tb);
+      integrableObjects[i]->lab2Body(Tb);
 
       // get the angular momentum, and propagate a half step
 
-      dAtom->getJ(ji);
+      integrableObjects[i]->getJ(ji);
 
       for (j = 0; j < 3; j++)
         ji[j] += (dt2 * Tb[j]) * eConvert;
 
-      this->rotationPropagation( dAtom, ji );
+      this->rotationPropagation( integrableObjects[i], ji );
 
-      dAtom->setJ(ji);
+      integrableObjects[i]->setJ(ji);
     }
   }
 
@@ -385,40 +398,38 @@ template<typename T> void Integrator<T>::moveB(void){
 
 template<typename T> void Integrator<T>::moveB(void){
   int i, j;
-  DirectionalAtom* dAtom;
   double Tb[3], ji[3];
   double vel[3], frc[3];
   double mass;
 
-  for (i = 0; i < nAtoms; i++){
-    atoms[i]->getVel(vel);
-    atoms[i]->getFrc(frc);
+  for (i = 0; i < integrableObjects.size(); i++){
+    integrableObjects[i]->getVel(vel);
+    integrableObjects[i]->getFrc(frc);
 
-    mass = atoms[i]->getMass();
+    mass = integrableObjects[i]->getMass();
 
     // velocity half step
     for (j = 0; j < 3; j++)
       vel[j] += (dt2 * frc[j] / mass) * eConvert;
 
-    atoms[i]->setVel(vel);
+    integrableObjects[i]->setVel(vel);
 
-    if (atoms[i]->isDirectional()){
-      dAtom = (DirectionalAtom *) atoms[i];
+    if (integrableObjects[i]->isDirectional()){
 
       // get and convert the torque to body frame
 
-      dAtom->getTrq(Tb);
-      dAtom->lab2Body(Tb);
+      integrableObjects[i]->getTrq(Tb);
+      integrableObjects[i]->lab2Body(Tb);
 
       // get the angular momentum, and propagate a half step
 
-      dAtom->getJ(ji);
+      integrableObjects[i]->getJ(ji);
 
       for (j = 0; j < 3; j++)
         ji[j] += (dt2 * Tb[j]) * eConvert;
 
 
-      dAtom->setJ(ji);
+      integrableObjects[i]->setJ(ji);
     }
   }
 
@@ -687,38 +698,56 @@ template<typename T> void Integrator<T>::rotationPropa
 }
 
 template<typename T> void Integrator<T>::rotationPropagation
-( DirectionalAtom* dAtom, double ji[3] ){
+( StuntDouble* sd, double ji[3] ){
 
   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
 
-  dAtom->getA(A);
-  dAtom->getI(I);
+  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 );
-
-  // rotate about the z-axis
-  angle = dt * ji[2] / I[2][2];
-  this->rotate( 0, 1, angle, ji, A);
+    angle = dt * ji[k] / I[k][k];
+    this->rotate( i, j, angle, ji, A);
 
-  // rotate about the y-axis
-  angle = dt2 * ji[1] / I[1][1];
-  this->rotate( 2, 0, angle, ji, A );
+    angle = dt2 * ji[j] / I[j][j];
+    this->rotate( k, i, angle, ji, A );
 
-  // rotate about the x-axis
-  angle = dt2 * ji[0] / I[0][0];
-  this->rotate( 1, 2, angle, ji, A );
-
-  dAtom->setA( 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  );
 }
 
 template<typename T> void Integrator<T>::rotate(int axes1, int axes2,