--- trunk/OOPSE/libmdtools/ZConstraint.cpp	2003/09/02 14:30:12	738
+++ trunk/OOPSE/libmdtools/ZConstraint.cpp	2003/09/25 19:27:15	787
@@ -2,8 +2,8 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
 #include "simError.h"
 #include <cmath>
 template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) 
-                                    : T(theInfo, the_ff), fz(NULL), curZPos(NULL), fzOut(NULL),
-                                 indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0)
+                                    : T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL),
+				      fzOut(NULL), curZconsTime(0), forcePolicy(NULL)
 {
 
   //get properties from SimInfo
@@ -213,7 +213,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
 
       //if user does not specify the zpos for the zconstraint molecule
       //its initial z coordinate  will be used as default
-      for(int i = 0; i < parameters->size(); i++){
+      for(int i = 0; i < (int)(parameters->size()); i++){
 
         if(!(*parameters)[i].havingZPos){
 #ifndef IS_MPI
@@ -227,7 +227,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
             //query which processor current zconstraint molecule belongs to
           int *MolToProcMap;
           int whichNode;
-    double initZPos;
+	  
           MolToProcMap = mpiSim->getMolToProcMap();
           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
         
@@ -279,8 +279,8 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
       zPos.push_back((*parameters)[searchResult].zPos);
 //       cout << "index: "<< (*parameters)[searchResult].zconsIndex 
 //              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; 
-      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
       
+      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
       molecules[i].getCOM(COM);
     }
     else
@@ -304,7 +304,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
   }
 
   //determine the states of z-constraint molecules
-  for(int i = 0; i < zconsMols.size(); i++){
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
     indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
 
     zconsMols[i]->getCOM(COM);
@@ -320,7 +320,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
   double totalMassOfUncons_local;
   totalMassOfUncons_local = 0;
   
-  for(int i = 0; i < unconsMols.size(); i++)
+  for(int i = 0; i < (int)(unconsMols.size()); i++)
     totalMassOfUncons_local += unconsMols[i]->getTotalMass();
     
 #ifndef IS_MPI
@@ -333,7 +333,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
   //get total number of unconstrained atoms
   int nUnconsAtoms_local;
   nUnconsAtoms_local = 0;
-  for(int i = 0; i < unconsMols.size(); i++)
+  for(int i = 0; i < (int)(unconsMols.size()); i++)
     nUnconsAtoms_local += unconsMols[i]->getNAtoms();
     
 #ifndef IS_MPI
@@ -394,7 +394,6 @@ template<typename T> void ZConstraint<T>::update()
       zconsMols.push_back(&molecules[i]);      
       zPos.push_back((*parameters)[index].zPos);
       kz.push_back((*parameters)[index].kRatio * zForceConst);
-      
       massOfZConsMols.push_back(molecules[i].getTotalMass());  
        
       molecules[i].getCOM(COM);
@@ -409,7 +408,7 @@ template<typename T> void ZConstraint<T>::update()
   }
 
   //determine the states of z-constraint molecules
-  for(int i = 0; i < zconsMols.size(); i++){
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
      zconsMols[i]->getCOM(COM);
       if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
       states.push_back(zcsFixed);
@@ -441,7 +440,7 @@ template<typename T> void ZConstraint<T>::update()
       simError();
     }
         
-    for(int i = 0; i < zconsMols.size(); i++){
+    for(int i = 0; i < (int)(zconsMols.size()); i++){
       indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
     }
 
@@ -560,7 +559,7 @@ template<typename T> void ZConstraint<T>::calcForce(in
 
   //write out forces and current positions of z-constraint molecules
   if(info->getTime() >= curZconsTime){    
-   for(int i = 0; i < zconsMols.size(); i++){
+   for(int i = 0; i < (int)(zconsMols.size()); i++){
       zconsMols[i]->getCOM(COM);
     curZPos[i] = COM[whichDirection];
 
@@ -655,7 +654,7 @@ template<typename T> void ZConstraint<T>::zeroOutVel()
 
   //zero out the velocities of center of mass of fixed z-constrained molecules
   
-  for(int i = 0; i < zconsMols.size(); i++){
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
 
     if (states[i] == zcsFixed){ 
 
@@ -696,12 +695,12 @@ template<typename T> void ZConstraint<T>::zeroOutVel()
   MVzOfMovingMols_local = 0;
   totalMassOfMovingZMols_local = 0;
 
-  for(int i =0; i < unconsMols.size(); i++){
+  for(int i =0; i < (int)(unconsMols.size()); i++){
     unconsMols[i]->getCOMvel(COMvel);
     MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];      
   } 
 
-  for(int i = 0; i < zconsMols.size(); i++){
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
     if (states[i] == zcsMoving){
       zconsMols[i]->getCOMvel(COMvel);
       MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];   
@@ -723,7 +722,7 @@ template<typename T> void ZConstraint<T>::zeroOutVel()
 
   //modify the velocites of unconstrained molecules  
   Atom** unconsAtoms;
-  for(int i = 0; i < unconsMols.size(); i++){
+  for(int i = 0; i < (int)(unconsMols.size()); i++){
   
     unconsAtoms = unconsMols[i]->getMyAtoms();
     for(int j = 0; j < unconsMols[i]->getNAtoms();j++){
@@ -736,7 +735,7 @@ template<typename T> void ZConstraint<T>::zeroOutVel()
 
   //modify the velocities of moving z-constrained molecuels
   Atom** movingZAtoms;
-  for(int i = 0; i < zconsMols.size(); i++){
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
 
     if (states[i] ==zcsMoving){
    
@@ -772,7 +771,6 @@ template<typename T> void ZConstraint<T>::doZconstrain
   Atom** zconsAtoms;
   double totalFZ; 
   double totalFZ_local;
-  double COMvel[3];   
   double COM[3];
   double force[3];
 
@@ -786,7 +784,7 @@ template<typename T> void ZConstraint<T>::doZconstrain
   //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
   //       << "total force is " << calcTotalForce() << endl;
 
-  for(int i = 0; i < zconsMols.size(); i++){
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
     
     if (states[i] == zcsFixed){
       
@@ -822,7 +820,7 @@ template<typename T> void ZConstraint<T>::doZconstrain
   force[1]= 0;
   force[2]= 0;
 
-  for(int i = 0; i < zconsMols.size(); i++){
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
 
     if (states[i] == zcsFixed){  
   
@@ -848,7 +846,7 @@ template<typename T> void ZConstraint<T>::doZconstrain
   force[2]= 0;
 
   //modify the forces of unconstrained molecules
-  for(int i = 0; i < unconsMols.size(); i++){
+  for(int i = 0; i < (int)(unconsMols.size()); i++){
      
      Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
      
@@ -861,7 +859,7 @@ template<typename T> void ZConstraint<T>::doZconstrain
   }      
 
  //modify the forces of moving z-constrained molecules
-  for(int i = 0; i < zconsMols.size(); i++) {
+  for(int i = 0; i < (int)(zconsMols.size()); i++) {
     if (states[i] == zcsMoving){
     
       Atom** movingZAtoms = zconsMols[i]->getMyAtoms();     
@@ -898,7 +896,7 @@ template<typename T> void ZConstraint<T>::doHarmonic()
 
   totalFZ_local = 0;
 
-  for(int i = 0; i < zconsMols.size(); i++) {
+  for(int i = 0; i < (int)(zconsMols.size()); i++) {
 
     if (states[i] == zcsMoving){
       zconsMols[i]->getCOM(COM);
@@ -932,15 +930,15 @@ template<typename T> void ZConstraint<T>::doHarmonic()
   MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
 #endif
 
-  cout << "before substracting harmonic force from moving molecuels "
-        << "total force is " << calcTotalForce()  << endl;
+  //cout << "before substracting harmonic force from moving molecuels "
+  //      << "total force is " << calcTotalForce()  << endl;
 
   force[0]= 0;
   force[1]= 0;
   force[2]= 0;
 
   //modify the forces of unconstrained molecules
-  for(int i = 0; i < unconsMols.size(); i++){
+  for(int i = 0; i < (int)(unconsMols.size()); i++){
      
      Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
      
@@ -951,8 +949,8 @@ template<typename T> void ZConstraint<T>::doHarmonic()
      }
   }   
 
-  cout << "after substracting harmonic force from moving molecuels "
-        << "total force is " << calcTotalForce()  << endl;
+  //cout << "after substracting harmonic force from moving molecuels "
+  //      << "total force is " << calcTotalForce()  << endl;
 
 }
 
@@ -969,7 +967,7 @@ template<typename T> bool ZConstraint<T>::checkZConsSt
   
   changed_local = 0;
   
-  for(int i =0; i < zconsMols.size(); i++){
+  for(int i =0; i < (int)(zconsMols.size()); i++){
 
     zconsMols[i]->getCOM(COM);
     diff = fabs(COM[whichDirection] - zPos[i]);  
@@ -1001,7 +999,7 @@ template<typename T> bool ZConstraint<T>::haveFixedZMo
 
   havingFixed_local = 0;
 
-  for(int i = 0; i < zconsMols.size(); i++)
+  for(int i = 0; i < (int)(zconsMols.size()); i++)
     if (states[i] == zcsFixed){
       havingFixed_local = 1;
     break;
@@ -1027,7 +1025,7 @@ template<typename T> bool ZConstraint<T>::haveMovingZM
 
   havingMoving_local = 0;
 
-  for(int i = 0; i < zconsMols.size(); i++)
+  for(int i = 0; i < (int)(zconsMols.size()); i++)
     if (states[i] == zcsMoving){
       havingMoving_local = 1;
     break;
@@ -1109,7 +1107,7 @@ template<typename T> double ZConstraint<T>::calcSysCOM
 
   massOfZCons_local = 0;
   
-  for(int i = 0; i < massOfZConsMols.size(); i++){
+  for(int i = 0; i < (int)(massOfZConsMols.size()); i++){
     massOfZCons_local += massOfZConsMols[i];
   }
 #ifndef IS_MPI
@@ -1160,7 +1158,7 @@ template<typename T> void ZConstraint<T>::PolicyByNumb
   int nMovingZAtoms;
   
   nMovingZAtoms_local = 0;
-  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
+  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
     if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
      nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
   
@@ -1198,7 +1196,7 @@ template<typename T> void ZConstraint<T>::PolicyByMass
   double massOfMovingZAtoms;
   
   massOfMovingZAtoms_local = 0;
-  for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++)
+  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
     if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
      massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();