--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/08/26 20:29:26	725
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2003/12/22 21:27:04	892
@@ -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"
 
@@ -25,7 +29,6 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   if (info->the_integrator != NULL){
     delete info->the_integrator;
   }
-  info->the_integrator = this;
 
   nAtoms = info->n_atoms;
 
@@ -147,56 +150,57 @@ 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;
   double statusTime = info->statusTime;
   double thermalTime = info->thermalTime;
+  double resetTime = info->resetTime;
 
+
   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();
+
   // initialize the forces before the first step
 
   calcForce(1, 1);
-  // myFF->doForces(1,1);
 
+  if (nConstrained){
+    preMove();
+    constrainA();
+    calcForce(1, 1);
+    constrainB();
+  }
+  
   if (info->setTemp){
     thermalize();
   }
 
-  calcPot = 0;
-  calcStress = 0;
-  currSample = sampleTime;
-  currThermal = thermalTime;
-  currStatus = statusTime;
-  
   calcPot     = 0;
   calcStress  = 0;
   currSample  = sampleTime + info->getTime();
   currThermal = thermalTime+ info->getTime();
   currStatus  = statusTime + info->getTime();
->>>>>>> 1.18
+  currReset   = resetTime  + info->getTime();
 
   dumpOut->writeDump(info->getTime());
   statOut->writeStat(info->getTime());
 
-  readyCheck();
 
 #ifdef IS_MPI
   strcpy(checkPointMsg, "The integrator is ready to go.");
@@ -209,8 +213,18 @@ 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){
@@ -226,20 +240,33 @@ 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){
+        this->resetIntegrator();
+        currReset += resetTime;
+      }
+    }
+    
+#ifdef PROFILE
+    endProfile( pro2 );
+#endif //profile
+
 #ifdef IS_MPI
     strcpy(checkPointMsg, "successfully took a time step.");
     MPIcheckPoint();
 #endif // is_mpi
   }
 
-  dumpOut->writeFinal(info->getTime());
 
+  // write the last frame
+  dumpOut->writeDump(info->getTime());
+
   delete dumpOut;
   delete statOut;
 }
@@ -247,13 +274,26 @@ 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();
 
+#ifdef PROFILE
+  endProfile(pro3);
+
+  startProfile(pro4);
+#endif // profile
+
   moveA();
 
-  if (nConstrained){
-    constrainA();
-  }
+#ifdef PROFILE
+  endProfile(pro4);
+  
+  startProfile(pro5);
+#endif//profile
 
 
 #ifdef IS_MPI
@@ -271,14 +311,19 @@ 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();
 
-  if (nConstrained){
-    constrainB();
-  }
+#ifdef PROFILE
+  endProfile(pro6);
+#endif // profile
 
 #ifdef IS_MPI
   strcpy(checkPointMsg, "Succesful moveB\n");
@@ -291,8 +336,6 @@ template<typename T> void Integrator<T>::moveA(void){
   int i, j;
   DirectionalAtom* dAtom;
   double Tb[3], ji[3];
-  double A[3][3], I[3][3];
-  double angle;
   double vel[3], pos[3], frc[3];
   double mass;
 
@@ -328,37 +371,15 @@ template<typename T> void Integrator<T>::moveA(void){
       for (j = 0; j < 3; j++)
         ji[j] += (dt2 * Tb[j]) * eConvert;
 
-      // use the angular velocities to propagate the rotation matrix a
-      // full time step
+      this->rotationPropagation( dAtom, ji );
 
-      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->setJ(ji);
-      dAtom->setA(A);
     }
   }
+
+  if (nConstrained){
+    constrainA();
+  }
 }
 
 
@@ -384,7 +405,7 @@ template<typename T> void Integrator<T>::moveB(void){
     if (atoms[i]->isDirectional()){
       dAtom = (DirectionalAtom *) atoms[i];
 
-      // get and convert the torque to body frame      
+      // get and convert the torque to body frame
 
       dAtom->getTrq(Tb);
       dAtom->lab2Body(Tb);
@@ -400,6 +421,10 @@ template<typename T> void Integrator<T>::moveB(void){
       dAtom->setJ(ji);
     }
   }
+
+  if (nConstrained){
+    constrainB();
+  }
 }
 
 template<typename T> void Integrator<T>::preMove(void){
@@ -418,7 +443,7 @@ 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];
@@ -558,10 +583,11 @@ template<typename T> void Integrator<T>::constrainA(){
     painCave.isFatal = 1;
     simError();
   }
+
 }
 
 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];
@@ -570,8 +596,7 @@ 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;
 
@@ -661,6 +686,41 @@ template<typename T> void Integrator<T>::rotate(int ax
   }
 }
 
+template<typename T> void Integrator<T>::rotationPropagation
+( DirectionalAtom* dAtom, double ji[3] ){
+
+  double angle;
+  double A[3][3], I[3][3];
+
+  // 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  );
+}
+
 template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
                                                 double angle, double ji[3],
                                                 double A[3][3]){
@@ -726,7 +786,7 @@ 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[][])
 
 
@@ -751,3 +811,13 @@ template<typename T> void Integrator<T>::thermalize(){
 template<typename T> void Integrator<T>::thermalize(){
   tStats->velocitize();
 }
+
+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();
+}