--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/09/24 19:34:39	784
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2004/06/21 18:52:21	1284
@@ -1,12 +1,17 @@
 #include <iostream>
-#include <cstdlib>
-#include <cmath>
-
+#include <stdlib.h>
+#include <math.h>
+#include "Rattle.hpp"
+#include "Roll.hpp"
 #ifdef IS_MPI
 #include "mpiSimulation.hpp"
 #include <unistd.h>
 #endif //is_mpi
 
+#ifdef PROFILE
+#include "mdProfile.hpp"
+#endif // profile
+
 #include "Integrator.hpp"
 #include "simError.h"
 
@@ -25,9 +30,20 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   if (info->the_integrator != NULL){
     delete info->the_integrator;
   }
-  
+
   nAtoms = info->n_atoms;
+  integrableObjects = info->integrableObjects;
 
+  consFramework = new RattleFramework(info);
+
+  if(consFramework == NULL){
+    sprintf(painCave.errMsg,
+      "Integrator::Intergrator() Error: Memory allocation error for RattleFramework" );
+    painCave.isFatal = 1;
+    simError();
+  }
+  
+/*
   // check for constraints
 
   constrainedA = NULL;
@@ -40,9 +56,13 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   nConstrained = 0;
 
   checkConstraints();
+*/
 }
 
 template<typename T> Integrator<T>::~Integrator(){
+  if (consFramework != NULL)
+    delete consFramework;
+/*
   if (nConstrained){
     delete[] constrainedA;
     delete[] constrainedB;
@@ -51,8 +71,10 @@ template<typename T> Integrator<T>::~Integrator(){
     delete[] moved;
     delete[] oldPos;
   }
+*/
 }
 
+/*
 template<typename T> void Integrator<T>::checkConstraints(void){
   isConstrained = 0;
 
@@ -64,7 +86,8 @@ 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();
 
@@ -86,7 +109,7 @@ template<typename T> void Integrator<T>::checkConstrai
       if (constrained){
         dummy_plug = theArray[j]->get_constraint();
         temp_con[nConstrained].set_a(dummy_plug->get_a());
-        temp_con[nConstrained].set_b(dummy_plug->get_b());
+        temp_con[nConstrained].set_b(Dummy_plug->get_b());
         temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
 
         nConstrained++;
@@ -110,6 +133,7 @@ template<typename T> void Integrator<T>::checkConstrai
     }
   }
 
+
   if (nConstrained > 0){
     isConstrained = 1;
 
@@ -131,7 +155,7 @@ 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;
 
@@ -143,10 +167,9 @@ template<typename T> void Integrator<T>::checkConstrai
 
   delete[] temp_con;
 }
+*/
 
-
 template<typename T> void Integrator<T>::integrate(void){
-  int i, j;                         // loop counters
 
   double runTime = info->run_time;
   double sampleTime = info->sampleTime;
@@ -154,37 +177,43 @@ template<typename T> void Integrator<T>::integrate(voi
   double thermalTime = info->thermalTime;
   double resetTime = info->resetTime;
 
-
+  double difference;
   double currSample;
   double currThermal;
   double currStatus;
   double currReset;
-  
+
   int calcPot, calcStress;
-  int isError;
 
   tStats = new Thermo(info);
   statOut = new StatWriter(info);
   dumpOut = new DumpWriter(info);
 
   atoms = info->atoms;
-  DirectionalAtom* dAtom;
 
   dt = info->dt;
   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->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  
+  //consFramework->doPreConstraint();
+  //consFramework->doConstrainA();
+  //calcForce(1, 1);
+  //consFramework->doConstrainB();
   
   if (info->setTemp){
     thermalize();
@@ -201,20 +230,30 @@ template<typename T> void Integrator<T>::integrate(voi
   statOut->writeStat(info->getTime());
 
 
-
 #ifdef IS_MPI
   strcpy(checkPointMsg, "The integrator is ready to go.");
   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;
     }
 
+#ifdef PROFILE
+    startProfile( pro1 );
+#endif
+    
     integrateStep(calcPot, calcStress);
 
+#ifdef PROFILE
+    endProfile( pro1 );
+
+    startProfile( pro2 );
+#endif // profile
+
     info->incrTime(dt);
 
     if (info->setTemp){
@@ -230,11 +269,11 @@ template<typename T> void Integrator<T>::integrate(voi
     }
 
     if (info->getTime() >= currStatus){
-      statOut->writeStat(info->getTime()); 
-      calcPot = 0; 
+      statOut->writeStat(info->getTime());
+      calcPot = 0;
       calcStress = 0;
       currStatus += statusTime;
-    } 
+    }
 
     if (info->resetIntegrator){
       if (info->getTime() >= currReset){
@@ -242,6 +281,10 @@ template<typename T> void Integrator<T>::integrate(voi
         currReset += resetTime;
       }
     }
+    
+#ifdef PROFILE
+    endProfile( pro2 );
+#endif //profile
 
 #ifdef IS_MPI
     strcpy(checkPointMsg, "successfully took a time step.");
@@ -249,7 +292,10 @@ template<typename T> void Integrator<T>::integrate(voi
 #endif // is_mpi
   }
 
-  dumpOut->writeFinal(info->getTime());
+  // dump out a file containing the omega values for the final configuration
+  if (info->useSolidThermInt && !info->useLiquidThermInt)
+    myFF->dumpzAngle();
+  
 
   delete dumpOut;
   delete statOut;
@@ -258,21 +304,35 @@ template<typename T> void Integrator<T>::integrateStep
 template<typename T> void Integrator<T>::integrateStep(int calcPot,
                                                        int calcStress){
   // Position full step, and velocity half step
-  preMove();
 
-  moveA();
+#ifdef PROFILE
+  startProfile(pro3);
+#endif //profile
 
+  //save old state (position, velocity etc)
+  consFramework->doPreConstraint();
 
+#ifdef PROFILE
+  endProfile(pro3);
 
+  startProfile(pro4);
+#endif // profile
 
+  moveA();
+
+#ifdef PROFILE
+  endProfile(pro4);
+  
+  startProfile(pro5);
+#endif//profile
+
+
 #ifdef IS_MPI
   strcpy(checkPointMsg, "Succesful moveA\n");
   MPIcheckPoint();
 #endif // is_mpi
 
-
   // calc forces
-
   calcForce(calcPot, calcStress);
 
 #ifdef IS_MPI
@@ -280,13 +340,20 @@ template<typename T> void Integrator<T>::integrateStep
   MPIcheckPoint();
 #endif // is_mpi
 
+#ifdef PROFILE
+  endProfile( pro5 );
 
+  startProfile( pro6 );
+#endif //profile
+
   // finish the velocity  half step
 
   moveB();
 
+#ifdef PROFILE
+  endProfile(pro6);
+#endif // profile
 
-
 #ifdef IS_MPI
   strcpy(checkPointMsg, "Succesful moveB\n");
   MPIcheckPoint();
@@ -295,19 +362,20 @@ 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;
+  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();
 
-  for (i = 0; i < nAtoms; i++){
-    atoms[i]->getVel(vel);
-    atoms[i]->getPos(pos);
-    atoms[i]->getFrc(frc);
-
-    mass = atoms[i]->getMass();
-
     for (j = 0; j < 3; j++){
       // velocity half step
       vel[j] += (dt2 * frc[j] / mass) * eConvert;
@@ -315,80 +383,74 @@ 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);
     }
   }
 
-  if (nConstrained){
-    constrainA();
-  }
+  consFramework->doConstrainA();
 }
 
 
 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      
+      // 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);
     }
   }
 
-  if (nConstrained){
-    constrainB();
-  }
+  consFramework->doConstrainB();
 }
 
+/*
 template<typename T> void Integrator<T>::preMove(void){
   int i, j;
   double pos[3];
@@ -405,7 +467,7 @@ template<typename T> void Integrator<T>::constrainA(){
 }
 
 template<typename T> void Integrator<T>::constrainA(){
-  int i, j, k;
+  int i, j;
   int done;
   double posA[3], posB[3];
   double velA[3], velB[3];
@@ -549,7 +611,7 @@ template<typename T> void Integrator<T>::constrainB(vo
 }
 
 template<typename T> void Integrator<T>::constrainB(void){
-  int i, j, k;
+  int i, j;
   int done;
   double posA[3], posB[3];
   double velA[3], velB[3];
@@ -558,8 +620,7 @@ template<typename T> void Integrator<T>::constrainB(vo
   int a, b, ax, ay, az, bx, by, bz;
   double rma, rmb;
   double dx, dy, dz;
-  double rabsq, pabsq, rvab;
-  double diffsq;
+  double rvab;
   double gab;
   int iteration;
 
@@ -648,40 +709,58 @@ template<typename T> void Integrator<T>::constrainB(vo
     simError();
   }
 }
-
+*/
 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);
-  
-  // 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];
-  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 );
-  
-  dAtom->setA( A  );    
+  sd->getA(A);
+  sd->getI(I);
+
+  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 );
+
+    angle = dt * ji[k] / I[k][k];
+    this->rotate( i, j, angle, ji, A);
+
+    angle = dt2 * ji[j] / I[j][j];
+    this->rotate( k, i, 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  );
 }
 
 template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
@@ -749,7 +828,7 @@ template<typename T> void Integrator<T>::rotate(int ax
     }
   }
 
-  // rotate the Rotation matrix acording to: 
+  // rotate the Rotation matrix acording to:
   //            A[][] = A[][] * transpose(rot[][])
 
 
@@ -778,3 +857,9 @@ template<typename T> double Integrator<T>::getConserve
 template<typename T> double Integrator<T>::getConservedQuantity(void){
   return tStats->getTotalE();
 }
+template<typename T> string Integrator<T>::getAdditionalParameters(void){
+  //By default, return a null string
+  //The reason we use string instead of char* is that if we use char*, we will
+  //return a pointer point to local variable which might cause problem
+  return string();
+}