--- trunk/OOPSE/libmdtools/Integrator.cpp	2003/10/28 16:03:37	829
+++ trunk/OOPSE/libmdtools/Integrator.cpp	2003/12/22 21:27:04	892
@@ -7,6 +7,10 @@
 #include <unistd.h>
 #endif //is_mpi
 
+#ifdef PROFILE
+#include "mdProfile.hpp"
+#endif // profile
+
 #include "Integrator.hpp"
 #include "simError.h"
 
@@ -25,7 +29,7 @@ template<typename T> Integrator<T>::Integrator(SimInfo
   if (info->the_integrator != NULL){
     delete info->the_integrator;
   }
-  
+
   nAtoms = info->n_atoms;
 
   // check for constraints
@@ -158,7 +162,7 @@ template<typename T> void Integrator<T>::integrate(voi
   double currThermal;
   double currStatus;
   double currReset;
-  
+
   int calcPot, calcStress;
 
   tStats = new Thermo(info);
@@ -179,7 +183,7 @@ template<typename T> void Integrator<T>::integrate(voi
   if (nConstrained){
     preMove();
     constrainA();
-    calcForce(1, 1);    
+    calcForce(1, 1);
     constrainB();
   }
   
@@ -198,7 +202,6 @@ template<typename T> void Integrator<T>::integrate(voi
   statOut->writeStat(info->getTime());
 
 
-
 #ifdef IS_MPI
   strcpy(checkPointMsg, "The integrator is ready to go.");
   MPIcheckPoint();
@@ -210,8 +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){
@@ -227,11 +240,11 @@ 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){
@@ -239,6 +252,10 @@ 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.");
@@ -257,13 +274,28 @@ 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();
@@ -279,12 +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();
-
 
+#ifdef PROFILE
+  endProfile(pro6);
+#endif // profile
 
 #ifdef IS_MPI
   strcpy(checkPointMsg, "Succesful moveB\n");
@@ -366,7 +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);
@@ -658,28 +697,28 @@ 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 +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[][])
 
 
@@ -776,3 +815,9 @@ 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();
+}