--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/09/23 20:34:31	782
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2003/10/29 17:55:28	841
@@ -1,6 +1,6 @@
 #include <iostream>
-#include <cstdlib>
-#include <cmath>
+#include <stdlib.h>
+#include <math.h>
 
 #ifdef IS_MPI
 #include "mpiSimulation.hpp"
@@ -25,7 +25,7 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   if (info->the_integrator != NULL){
     delete info->the_integrator;
   }
-  
+
   nAtoms = info->n_atoms;
 
   // check for constraints
@@ -146,7 +146,6 @@ 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;
@@ -159,31 +158,36 @@ 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
 
+  std::cerr << "Before initial Force calc\n";
+
   calcForce(1, 1);
 
   if (nConstrained){
     preMove();
     constrainA();
-    calcForce(1, 1);    
+    calcForce(1, 1);
     constrainB();
+    std::cerr << "premove done\n";
   }
-  
+
+
+
   if (info->setTemp){
     thermalize();
   }
@@ -198,8 +202,8 @@ 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.");
   MPIcheckPoint();
@@ -228,11 +232,11 @@ 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){
@@ -241,14 +245,18 @@ template<typename T> void Integrator<T>::integrate(voi
       }
     }
 
+    std::cerr << "done with time = " << info->getTime() << "\n";
+
 #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;
 }
@@ -365,7 +373,7 @@ 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);
@@ -403,7 +411,7 @@ 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 +555,7 @@ 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 +564,7 @@ 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;
 
@@ -658,28 +665,28 @@ template<typename T> void Integrator<T>::rotationPropa
 
   dAtom->getA(A);
   dAtom->getI(I);
-  
-  // rotate about the x-axis      
+
+  // 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  );    
+
+  dAtom->setA( A  );
 }
 
 template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
@@ -747,7 +754,7 @@ 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 +783,9 @@ 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();
+}