--- trunk/OOPSE/libmdtools/Integrator.cpp	2004/04/20 16:56:40	1127
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2004/06/04 03:15:31	1234
@@ -1,7 +1,7 @@
 #include <iostream>
 #include <stdlib.h>
 #include <math.h>
-
+#include "Rattle.hpp"
 #ifdef IS_MPI
 #include "mpiSimulation.hpp"
 #include <unistd.h>
@@ -33,6 +33,16 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   nAtoms = info->n_atoms;
   integrableObjects = info->integrableObjects;
 
+  rattle = new RattleFramework(info);
+
+  if(rattle == NULL){
+    sprintf(painCave.errMsg,
+      "Integrator::Intergrator() Error: Memory allocation error for RattleFramework" );
+    painCave.isFatal = 1;
+    simError();
+  }
+  
+/*
   // check for constraints
 
   constrainedA = NULL;
@@ -45,9 +55,13 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   nConstrained = 0;
 
   checkConstraints();
+*/
 }
 
 template<typename T> Integrator<T>::~Integrator(){
+  if (rattle != NULL)
+    delete rattle;
+/*
   if (nConstrained){
     delete[] constrainedA;
     delete[] constrainedB;
@@ -56,8 +70,10 @@ template<typename T> Integrator<T>::~Integrator(){
     delete[] moved;
     delete[] oldPos;
   }
+*/
 }
 
+/*
 template<typename T> void Integrator<T>::checkConstraints(void){
   isConstrained = 0;
 
@@ -150,8 +166,8 @@ template<typename T> void Integrator<T>::checkConstrai
 
   delete[] temp_con;
 }
+*/
 
-
 template<typename T> void Integrator<T>::integrate(void){
 
   double runTime = info->run_time;
@@ -160,7 +176,7 @@ template<typename T> void Integrator<T>::integrate(voi
   double thermalTime = info->thermalTime;
   double resetTime = info->resetTime;
 
-
+  double difference;
   double currSample;
   double currThermal;
   double currStatus;
@@ -183,16 +199,20 @@ template<typename T> void Integrator<T>::integrate(voi
   // 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();
-    calcForce(1, 1);
-    constrainB();
-  }
+
+  //execute constraint algorithm to make sure at the very beginning the system is constrained  
+  rattle->doPreConstraint();
+  rattle->doRattleA();
+  calcForce(1, 1);
+  rattle->doRattleB();
   
   if (info->setTemp){
     thermalize();
@@ -215,7 +235,8 @@ 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;
     }
@@ -270,6 +291,11 @@ 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();
+  
+
   delete dumpOut;
   delete statOut;
 }
@@ -282,7 +308,8 @@ template<typename T> void Integrator<T>::integrateStep
   startProfile(pro3);
 #endif //profile
 
-  preMove();
+  //save old state (position, velocity etc)
+  rattle->doPreConstraint();
 
 #ifdef PROFILE
   endProfile(pro3);
@@ -304,9 +331,7 @@ template<typename T> void Integrator<T>::integrateStep
   MPIcheckPoint();
 #endif // is_mpi
 
-
   // calc forces
-
   calcForce(calcPot, calcStress);
 
 #ifdef IS_MPI
@@ -341,6 +366,7 @@ 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);
@@ -379,9 +405,7 @@ template<typename T> void Integrator<T>::moveA(void){
     }
   }
 
-  if (nConstrained){
-    constrainA();
-  }
+  rattle->doRattleA();
 }
 
 
@@ -422,11 +446,10 @@ template<typename T> void Integrator<T>::moveB(void){
     }
   }
 
-  if (nConstrained){
-    constrainB();
-  }
+  rattle->doRattleB();
 }
 
+/*
 template<typename T> void Integrator<T>::preMove(void){
   int i, j;
   double pos[3];
@@ -685,7 +708,7 @@ template<typename T> void Integrator<T>::constrainB(vo
     simError();
   }
 }
-
+*/
 template<typename T> void Integrator<T>::rotationPropagation
 ( StuntDouble* sd, double ji[3] ){
 
@@ -724,6 +747,7 @@ template<typename T> void Integrator<T>::rotationPropa
     
     // 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