--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/09/23 20:34:31	782
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2004/04/12 20:32:20	1097
@@ -1,12 +1,16 @@
 #include <iostream>
-#include <cstdlib>
-#include <cmath>
+#include <stdlib.h>
+#include <math.h>
 
 #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"
 
@@ -25,8 +29,9 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   if (info->the_integrator != NULL){
     delete info->the_integrator;
   }
-  
+
   nAtoms = info->n_atoms;
+  integrableObjects = info->integrableObjects;
 
   // check for constraints
 
@@ -64,7 +69,8 @@ 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();
 
@@ -110,6 +116,7 @@ template<typename T> void Integrator<T>::checkConstrai
     }
   }
 
+
   if (nConstrained > 0){
     isConstrained = 1;
 
@@ -131,7 +138,7 @@ 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;
 
@@ -146,7 +153,6 @@ template<typename T> void Integrator<T>::integrate(voi
 
 
 template<typename T> void Integrator<T>::integrate(void){
-  int i, j;                         // loop counters
 
   double runTime = info->run_time;
   double sampleTime = info->sampleTime;
@@ -159,28 +165,31 @@ template<typename T> void Integrator<T>::integrate(voi
   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();
+
   // initialize the forces before the first step
 
   calcForce(1, 1);
 
+  //temp test
+  tStats->getPotential();
+  
   if (nConstrained){
     preMove();
     constrainA();
-    calcForce(1, 1);    
+    calcForce(1, 1);
     constrainB();
   }
   
@@ -198,7 +207,6 @@ template<typename T> void Integrator<T>::integrate(voi
   dumpOut->writeDump(info->getTime());
   statOut->writeStat(info->getTime());
 
-  readyCheck();
 
 #ifdef IS_MPI
   strcpy(checkPointMsg, "The integrator is ready to go.");
@@ -211,8 +219,18 @@ template<typename T> void Integrator<T>::integrate(voi
       calcStress = 1;
     }
 
+#ifdef PROFILE
+    startProfile( pro1 );
+#endif
+    
     integrateStep(calcPot, calcStress);
 
+#ifdef PROFILE
+    endProfile( pro1 );
+
+    startProfile( pro2 );
+#endif // profile
+
     info->incrTime(dt);
 
     if (info->setTemp){
@@ -228,11 +246,11 @@ 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){
@@ -240,6 +258,10 @@ 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.");
@@ -247,8 +269,6 @@ template<typename T> void Integrator<T>::integrate(voi
 #endif // is_mpi
   }
 
-  dumpOut->writeFinal(info->getTime());
-
   delete dumpOut;
   delete statOut;
 }
@@ -256,13 +276,28 @@ 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
+
+#ifdef PROFILE
+  startProfile(pro3);
+#endif //profile
+
   preMove();
 
-  moveA();
+#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();
@@ -278,13 +313,20 @@ 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();
@@ -293,18 +335,18 @@ 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);
-
-    mass = atoms[i]->getMass();
+ 
+  for (i = 0; i < integrableObjects.size() ; i++){
+    integrableObjects[i]->getVel(vel);
+    integrableObjects[i]->getPos(pos);
+    integrableObjects[i]->getFrc(frc);
+    
+    mass = integrableObjects[i]->getMass();
 
     for (j = 0; j < 3; j++){
       // velocity half step
@@ -313,27 +355,26 @@ 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);
     }
   }
 
@@ -345,40 +386,38 @@ 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      
+      // 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);
     }
   }
 
@@ -403,7 +442,7 @@ 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];
@@ -547,7 +586,7 @@ 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];
@@ -556,8 +595,7 @@ 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;
 
@@ -648,7 +686,7 @@ 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];
@@ -656,30 +694,30 @@ template<typename T> void Integrator<T>::rotationPropa
   // use the angular velocities to propagate the rotation matrix a
   // full time step
 
-  dAtom->getA(A);
-  dAtom->getI(I);
-  
-  // rotate about the x-axis      
+  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 ); 
-  
+  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->setA( A  );
 }
 
 template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
@@ -747,7 +785,7 @@ 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[][])
 
 
@@ -776,3 +814,9 @@ 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();
+}