--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/09/22 23:07:57	781
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2003/10/28 16:03:37	829
@@ -1,6 +1,6 @@
 #include <iostream>
-#include <cstdlib>
-#include <cmath>
+#include <stdlib.h>
+#include <math.h>
 
 #ifdef IS_MPI
 #include "mpiSimulation.hpp"
@@ -25,8 +25,7 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   if (info->the_integrator != NULL){
     delete info->the_integrator;
   }
-  info->the_integrator = this;
-
+  
   nAtoms = info->n_atoms;
 
   // check for constraints
@@ -147,7 +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;
@@ -162,18 +160,18 @@ template<typename T> void Integrator<T>::integrate(voi
   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);
@@ -199,8 +197,8 @@ 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();
@@ -248,8 +246,10 @@ template<typename T> void Integrator<T>::integrate(voi
 #endif // is_mpi
   }
 
-  dumpOut->writeFinal(info->getTime());
 
+  // write the last frame
+  dumpOut->writeDump(info->getTime());
+
   delete dumpOut;
   delete statOut;
 }
@@ -404,7 +404,7 @@ 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];
@@ -548,7 +548,7 @@ 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];
@@ -557,8 +557,7 @@ 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;