--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/07/14 22:38:13	600
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2003/08/11 19:41:36	677
@@ -11,7 +11,7 @@ Integrator::Integrator( SimInfo *theInfo, ForceFields*
 #include "simError.h"
 
 
-Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){
+template<typename T> Integrator<T>::Integrator( SimInfo *theInfo, ForceFields* the_ff ) {
   
   info = theInfo;
   myFF = the_ff;
@@ -27,8 +27,6 @@ Integrator::Integrator( SimInfo *theInfo, ForceFields*
 
   nAtoms = info->n_atoms;
 
-  std::cerr << "integ nAtoms = "  << nAtoms << "\n";
-
   // check for constraints
   
   constrainedA    = NULL;
@@ -43,7 +41,7 @@ Integrator::~Integrator() {
   checkConstraints();
 }
 
-Integrator::~Integrator() {
+template<typename T> Integrator<T>::~Integrator() {
   
   if( nConstrained ){
     delete[] constrainedA;
@@ -56,7 +54,7 @@ void Integrator::checkConstraints( void ){
   
 }
 
-void Integrator::checkConstraints( void ){
+template<typename T> void Integrator<T>::checkConstraints( void ){
 
 
   isConstrained = 0;
@@ -75,12 +73,7 @@ void Integrator::checkConstraints( void ){
       
       constrained = theArray[j]->is_constrained();
 
-      std::cerr << "Is the folowing bond constrained \n";
-      theArray[j]->printMe();
-      
       if(constrained){
-	
-	std::cerr << "Yes\n";
 
 	dummy_plug = theArray[j]->get_constraint();
 	temp_con[nConstrained].set_a( dummy_plug->get_a() );
@@ -90,7 +83,6 @@ void Integrator::checkConstraints( void ){
 	nConstrained++;
 	constrained = 0;
       } 
-      else std::cerr << "No.\n";
     }
 
     theArray = (SRI**) molecules[i].getMyBends();
@@ -163,7 +155,7 @@ void Integrator::integrate( void ){
 }
 
 
-void Integrator::integrate( void ){
+template<typename T> void Integrator<T>::integrate( void ){
 
   int i, j;                         // loop counters
 
@@ -175,7 +167,6 @@ void Integrator::integrate( void ){
   double currSample;
   double currThermal;
   double currStatus;
-  double currTime;
 
   int calcPot, calcStress;
   int isError;
@@ -192,23 +183,21 @@ void Integrator::integrate( void ){
 
   // initialize the forces before the first step
 
-  myFF->doForces(1,1);
+  calcForce(1, 1);
   
   if( info->setTemp ){
     
-    tStats->velocitize();
+    thermalize();
   }
   
-  dumpOut->writeDump( 0.0 );
-  statOut->writeStat( 0.0 );
-  
   calcPot     = 0;
   calcStress  = 0;
   currSample  = sampleTime;
   currThermal = thermalTime;
   currStatus  = statusTime;
-  currTime    = 0.0;;
 
+  dumpOut->writeDump( info->getTime() );
+  statOut->writeStat( info->getTime() );
 
   readyCheck();
 
@@ -218,33 +207,31 @@ void Integrator::integrate( void ){
   MPIcheckPoint();
 #endif // is_mpi
 
-  while( currTime < runTime ){
+  while( info->getTime() < runTime ){
 
-    if( (currTime+dt) >= currStatus ){
+    if( (info->getTime()+dt) >= currStatus ){
       calcPot = 1;
       calcStress = 1;
     }
 
-    std::cerr << currTime << "\n";
-
     integrateStep( calcPot, calcStress );
       
-    currTime += dt;
+    info->incrTime(dt);
 
     if( info->setTemp ){
-      if( currTime >= currThermal ){
-	tStats->velocitize();
+      if( info->getTime() >= currThermal ){
+	thermalize();
 	currThermal += thermalTime;
       }
     }
 
-    if( currTime >= currSample ){
-      dumpOut->writeDump( currTime );
+    if( info->getTime() >= currSample ){
+      dumpOut->writeDump( info->getTime() );
       currSample += sampleTime;
     }
 
-    if( currTime >= currStatus ){ 
-      statOut->writeStat( currTime ); 
+    if( info->getTime() >= currStatus ){ 
+      statOut->writeStat( info->getTime() ); 
       calcPot = 0; 
       calcStress = 0;
       currStatus += statusTime;
@@ -258,13 +245,13 @@ void Integrator::integrate( void ){
 
   }
 
-  dumpOut->writeFinal(currTime);
+  dumpOut->writeFinal(info->getTime());
 
   delete dumpOut;
   delete statOut;
 }
 
-void Integrator::integrateStep( int calcPot, int calcStress ){
+template<typename T> void Integrator<T>::integrateStep( int calcPot, int calcStress ){
 
 
       
@@ -274,19 +261,38 @@ void Integrator::integrateStep( int calcPot, int calcS
   moveA();
   if( nConstrained ) constrainA();
 
+  
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Succesful moveA\n" );
+  MPIcheckPoint();
+#endif // is_mpi
+  
+
   // calc forces
 
-  myFF->doForces(calcPot,calcStress);
+  calcForce(calcPot,calcStress);
 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Succesful doForces\n" );
+  MPIcheckPoint();
+#endif // is_mpi
+  
+
   // finish the velocity  half step
   
   moveB();
   if( nConstrained ) constrainB();
-   
+  
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Succesful moveB\n" );
+  MPIcheckPoint();
+#endif // is_mpi
+  
+ 
 }
 
 
-void Integrator::moveA( void ){
+template<typename T> void Integrator<T>::moveA( void ){
   
   int i, j;
   DirectionalAtom* dAtom;
@@ -365,7 +371,7 @@ void Integrator::moveB( void ){
 }
 
 
-void Integrator::moveB( void ){
+template<typename T> void Integrator<T>::moveB( void ){
   int i, j;
   DirectionalAtom* dAtom;
   double Tb[3], ji[3];
@@ -407,7 +413,7 @@ void Integrator::preMove( void ){
   }
 }
 
-void Integrator::preMove( void ){
+template<typename T> void Integrator<T>::preMove( void ){
   int i, j;
   double pos[3];
 
@@ -425,7 +431,7 @@ void Integrator::constrainA(){
   }  
 }
 
-void Integrator::constrainA(){
+template<typename T> void Integrator<T>::constrainA(){
 
   int i,j,k;
   int done;
@@ -576,7 +582,7 @@ void Integrator::constrainB( void ){
 
 }
 
-void Integrator::constrainB( void ){
+template<typename T> void Integrator<T>::constrainB( void ){
   
   int i,j,k;
   int done;
@@ -685,7 +691,7 @@ void Integrator::rotate( int axes1, int axes2, double 
 
 }
 
-void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], 
+template<typename T> void Integrator<T>::rotate( int axes1, int axes2, double angle, double ji[3], 
 			 double A[3][3] ){
 
   int i,j,k;
@@ -766,3 +772,12 @@ void Integrator::rotate( int axes1, int axes2, double 
     }
   }
 }
+
+template<typename T> void Integrator<T>::calcForce( int calcPot, int calcStress ){
+   myFF->doForces(calcPot,calcStress);
+  
+}
+
+template<typename T> void Integrator<T>::thermalize(){
+  tStats->velocitize();  
+}