--- trunk/OOPSE/libmdtools/ZConstraint.cpp	2003/08/13 19:21:53	693
+++ trunk/OOPSE/libmdtools/ZConstraint.cpp	2003/10/28 16:03:37	829
@@ -1,9 +1,9 @@
 #include "Integrator.hpp"
 #include "simError.h"
-#include <cmath>
+#include <math.h>
 template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) 
-                                    : T(theInfo, the_ff), fz(NULL), 
-				      indexOfZConsMols(NULL)
+                                    : T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL),
+				      fzOut(NULL), curZconsTime(0), forcePolicy(NULL)
 {
 
   //get properties from SimInfo
@@ -11,6 +11,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
   ZConsParaData* zConsParaData;
   DoubleData* sampleTime;
   DoubleData* tolerance;
+  StringData* policy;
   StringData* filename; 
   double COM[3];
 
@@ -26,6 +27,46 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
   double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2;
   zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox);
 
+  //creat force Subtraction policy
+  data = info->getProperty(ZCONSFORCEPOLICY_ID);
+  if(!data){
+    sprintf( painCave.errMsg,
+               "ZConstraint Warning: User does not set force Subtraction policy, "
+               "PolicyByMass is used\n");
+    painCave.isFatal = 0;
+    simError();      
+
+    forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
+  }
+  else{
+    policy = dynamic_cast<StringData*>(data);
+    
+    if(!policy){
+      sprintf( painCave.errMsg,
+                 "ZConstraint Error: Convertion from GenericData to StringData failure, "
+                 "PolicyByMass is used\n");
+      painCave.isFatal = 0;
+      simError();      
+
+      forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
+    }
+    else{
+      if(policy->getData() == "BYNUMBER")
+        forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this);
+      else if(policy->getData() == "BYMASS")
+        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
+      else{
+        sprintf( painCave.errMsg,
+                  "ZConstraint Warning: unknown force Subtraction policy, "
+                  "PolicyByMass is used\n");
+        painCave.isFatal = 0;
+        simError();      
+        forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this);
+      }   
+    }
+  }
+  
+  
   //retrieve sample time of z-contraint 
   data = info->getProperty(ZCONSTIME_ID);
   
@@ -69,7 +110,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
   }
   else{
 
-     filename = dynamic_cast<StringData*>(data);
+    filename = dynamic_cast<StringData*>(data);
     
     if(!filename){
 
@@ -83,7 +124,6 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
       this->zconsOutput = filename->getData();
     }
     
-
   }
 
   //retrieve tolerance for z-constraint molecuels
@@ -113,7 +153,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
     }
 
   }
-	
+  
   //retrieve index of z-constraint molecules
   data = info->getProperty(ZCONSPARADATA_ID);
   if(!data) {
@@ -154,7 +194,7 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
                "ZConstraint error: index is out of range\n");
         painCave.isFatal = 1;
         simError(); 
-      	}
+        }
 
       maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
 
@@ -173,52 +213,51 @@ 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){
-
+        if(!(*parameters)[i].havingZPos){
 #ifndef IS_MPI
-            for(int j = 0; j < nMols; j++){
-              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
-                 molecules[j].getCOM(COM);
-		          break; 
-              }
+          for(int j = 0; j < nMols; j++){
+            if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
+              molecules[j].getCOM(COM);
+        break; 
             }
+          }
 #else
             //query which processor current zconstraint molecule belongs to
-           int *MolToProcMap;
-           int whichNode;
-			 double initZPos;
-           MolToProcMap = mpiSim->getMolToProcMap();
-           whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
-			  
-           //broadcast the zpos of current z-contraint molecule
-           //the node which contain this 
+          int *MolToProcMap;
+          int whichNode;
+	  
+          MolToProcMap = mpiSim->getMolToProcMap();
+          whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
+        
+          //broadcast the zpos of current z-contraint molecule
+          //the node which contain this 
            
-           if (worldRank == whichNode ){
-					 	
-             for(int j = 0; j < nMols; j++)
-               if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
-                 molecules[j].getCOM(COM);
-					 break; 
-               }
-				 
-           }
+          if (worldRank == whichNode ){
+            
+            for(int j = 0; j < nMols; j++)
+              if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
+                molecules[j].getCOM(COM);
+          break; 
+              }
+         
+          }
 
-            MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);			  
+          MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);        
 #endif
             
-	         (*parameters)[i].zPos = COM[whichDirection];
+          (*parameters)[i].zPos = COM[whichDirection];
 
-            sprintf( painCave.errMsg,
-                     "ZConstraint warningr: Does not specify zpos for z-constraint molecule "
+          sprintf( painCave.errMsg,
+                     "ZConstraint warning: Does not specify zpos for z-constraint molecule "
                      "initial z coornidate will be used \n");
-            painCave.isFatal = 0;
-            simError();  
-	  
-	      }
-	    }
-			
+           painCave.isFatal = 0;
+           simError();  
+    
+  }
+      }
+      
     }//end if (!zConsParaData)
   }//end  if (!data)
              
@@ -238,8 +277,10 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
       massOfZConsMols.push_back(molecules[i].getTotalMass());  
 
       zPos.push_back((*parameters)[searchResult].zPos);
-	   kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
+//       cout << "index: "<< (*parameters)[searchResult].zconsIndex 
+//              <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; 
       
+      kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
       molecules[i].getCOM(COM);
     }
     else
@@ -252,9 +293,10 @@ template<typename T> ZConstraint<T>::ZConstraint(SimIn
   }
 
   fz = new double[zconsMols.size()];
+  curZPos = new double[zconsMols.size()]; 
   indexOfZConsMols = new int [zconsMols.size()];
 
-  if(!fz || !indexOfZConsMols){
+  if(!fz || !curZPos || !indexOfZConsMols){
     sprintf( painCave.errMsg,
              "Memory allocation failure in class Zconstraint\n");
     painCave.isFatal = 1;
@@ -262,14 +304,14 @@ 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);
+    zconsMols[i]->getCOM(COM);
     if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
-		states.push_back(zcsFixed);
-	 else
-		states.push_back(zcsMoving);
+      states.push_back(zcsFixed);
+    else
+      states.push_back(zcsMoving);
   }
   
 #endif 
@@ -278,52 +320,55 @@ 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
   totalMassOfUncons = totalMassOfUncons_local;
 #else
-  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
+  MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1,
+                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
 #endif
 
-
   //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
   totNumOfUnconsAtoms = nUnconsAtoms_local;
 #else
-  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
+  MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, 
+                      MPI_INT,MPI_SUM, MPI_COMM_WORLD);  
 #endif  
 
-  // creat zconsWriter  
-  fzOut = new ZConsWriter(zconsOutput.c_str());   
-  
-  if(!fzOut){
-    sprintf( painCave.errMsg,
-             "Memory allocation failure in class Zconstraint\n");
-    painCave.isFatal = 1;
-    simError();
-  }
-  
+  forcePolicy->update();
 }
 
 template<typename T> ZConstraint<T>::~ZConstraint()
 {
   if(fz)
     delete[] fz;
+
+  if(curZPos)
+    delete[] curZPos;
   
   if(indexOfZConsMols)
     delete[] indexOfZConsMols;
   
   if(fzOut)
     delete fzOut;
+  
+  if(forcePolicy)
+    delete forcePolicy;
 }
 
+
+/**
+ * 
+ */
+
 #ifdef IS_MPI
 template<typename T> void ZConstraint<T>::update()
 {
@@ -348,8 +393,7 @@ 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);
-			
+      kz.push_back((*parameters)[index].kRatio * zForceConst);
       massOfZConsMols.push_back(molecules[i].getTotalMass());  
        
       molecules[i].getCOM(COM);
@@ -364,12 +408,12 @@ template<typename T> void ZConstraint<T>::update()
   }
 
   //determine the states of z-constraint molecules
-  for(int i = 0; i < zconsMols.size(); i++){
-	   zconsMols[i]->getCOM(COM);
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
+     zconsMols[i]->getCOM(COM);
       if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
-		  states.push_back(zcsFixed);
-	   else
-		  states.push_back(zcsMoving);
+      states.push_back(zcsFixed);
+     else
+      states.push_back(zcsMoving);
   }
 
     
@@ -377,41 +421,50 @@ template<typename T> void ZConstraint<T>::update()
   // that we want to make the MPI communication simple
   if(fz)
     delete[] fz;
+  
+  if(curZPos)
+    delete[] curZPos;
     
   if(indexOfZConsMols)
     delete[] indexOfZConsMols;
     
   if (zconsMols.size() > 0){
     fz = new double[zconsMols.size()];
+   curZPos = new double[zconsMols.size()];
     indexOfZConsMols =  new int[zconsMols.size()];
     
-    if(!fz || !indexOfZConsMols){
+    if(!fz || !curZPos || !indexOfZConsMols){
       sprintf( painCave.errMsg,
                "Memory allocation failure in class Zconstraint\n");
       painCave.isFatal = 1;
       simError();
     }
         
-    for(int i = 0; i < zconsMols.size(); i++){
+    for(int i = 0; i < (int)(zconsMols.size()); i++){
       indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
     }
 
   }
   else{
     fz = NULL;
+   curZPos = NULL;
     indexOfZConsMols = NULL;
   }
   
+  //
+  forcePolicy->update();
+  
 }
 
 #endif
 
-/**  Function Name: isZConstraintMol
- **  Parameter
- **    Molecule* mol
- **  Return value:
- **    -1, if the molecule is not z-constraint molecule, 
- **    other non-negative values, its index in indexOfAllZConsMols vector
+/**
+ *  Function Name: isZConstraintMol
+ *  Parameter
+ *    Molecule* mol
+ *  Return value:
+ *    -1, if the molecule is not z-constraint molecule, 
+ *    other non-negative values, its index in indexOfAllZConsMols vector
  */
 
 template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
@@ -441,10 +494,22 @@ template<typename T> void ZConstraint<T>::integrate(){
 }
 
 template<typename T> void ZConstraint<T>::integrate(){
+
+  // creat zconsWriter  
+  fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);   
   
+  if(!fzOut){
+    sprintf( painCave.errMsg,
+             "Memory allocation failure in class Zconstraint\n");
+    painCave.isFatal = 1;
+    simError();
+  }
+  
   //zero out the velocities of center of mass of unconstrained molecules 
   //and the velocities of center of mass of every single z-constrained molecueles
   zeroOutVel();
+
+  curZconsTime = zconsTime + info->getTime();
   
   T::integrate();
 
@@ -456,36 +521,77 @@ template<typename T> void ZConstraint<T>::integrate(){
  *
  *
  *
- */
-
- 
+ */ 
 template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
   double zsys;
+  double COM[3];
+  double force[3];
+  double zSysCOMVel;
 
   T::calcForce(calcPot, calcStress);
 
-  if (checkZConsState())
-  zeroOutVel();
+  if (checkZConsState()){    
+    zeroOutVel();    
+    forcePolicy->update();
+  }  
   
   zsys = calcZSys();
-  cout << "---------------------------------------------------------------------" <<endl;
-  cout << "current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;   	 
-  cout << "before calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
-	
+  zSysCOMVel = calcSysCOMVel();
+#ifdef IS_MPI
+  if(worldRank == 0){
+#endif
+     //cout << "---------------------------------------------------------------------" <<endl;
+     //cout << "current time: " << info->getTime() << endl;
+     //cout << "center of mass at z: " << zsys << endl;     
+     //cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
 
+#ifdef IS_MPI
+  }
+#endif
+
   //do zconstraint force; 
   if (haveFixedZMols())
     this->doZconstraintForce();
 
-
-      
   //use harmonical poteintial to move the molecules to the specified positions
   if (haveMovingZMols())
     this->doHarmonic();
-   
-  fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
-  cout << "after calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl; 
+
+  //write out forces and current positions of z-constraint molecules
+  if(info->getTime() >= curZconsTime){    
+   for(int i = 0; i < (int)(zconsMols.size()); i++){
+      zconsMols[i]->getCOM(COM);
+    curZPos[i] = COM[whichDirection];
+
+    //if the z-constraint molecule is still moving, just record its force
+    if(states[i] == zcsMoving){
+         fz[i] = 0;
+      Atom** movingZAtoms;
+      movingZAtoms = zconsMols[i]->getMyAtoms();
+      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
+           movingZAtoms[j]->getFrc(force);
+           fz[i] += force[whichDirection];
+      }
+     }
+   }
+    fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos);
+   curZconsTime += zconsTime;
+  }
+
+  zSysCOMVel = calcSysCOMVel();  
+#ifdef IS_MPI
+  if(worldRank == 0){
+#endif
+     //cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
+#ifdef IS_MPI
+  }
+#endif
 }
+
+
+/**
+ * 
+ */
  
 template<typename T> double ZConstraint<T>::calcZSys()
 {
@@ -494,16 +600,11 @@ template<typename T> double ZConstraint<T>::calcZSys()
   double totalMass;
   double totalMZ_local;
   double totalMZ;
-  double massOfUncons_local;
   double massOfCurMol;
   double COM[3];
   
   totalMass_local = 0;
-  totalMass = 0;
   totalMZ_local = 0;
-  totalMZ = 0;
-  massOfUncons_local = 0;
-    
   
   for(int i = 0; i < nMols; i++){
     massOfCurMol = molecules[i].getTotalMass(); 
@@ -511,24 +612,19 @@ template<typename T> double ZConstraint<T>::calcZSys()
      
     totalMass_local += massOfCurMol;
     totalMZ_local += massOfCurMol * COM[whichDirection];
-    
-    if(isZConstraintMol(&molecules[i]) == -1){
-    
-      massOfUncons_local += massOfCurMol;
-    }  
-    
+
   }
+ 
   
-  
 #ifdef IS_MPI  
-  MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
-  MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);  
-  MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
-#else
+  MPI_Allreduce(&totalMass_local, &totalMass, 1, 
+                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
+  MPI_Allreduce(&totalMZ_local, &totalMZ, 1,
+                      MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);  
+ #else
   totalMass = totalMass_local;
   totalMZ = totalMZ_local;
-  totalMassOfUncons = massOfUncons_local;
-#endif  
+ #endif  
 
   double zsys;
   zsys = totalMZ / totalMass;
@@ -547,8 +643,6 @@ template<typename T> void ZConstraint<T>::thermalize( 
 
 /**
  *
- *
- *
  */
 
 template<typename T> void ZConstraint<T>::zeroOutVel(){
@@ -556,43 +650,42 @@ template<typename T> void ZConstraint<T>::zeroOutVel()
   Atom** fixedZAtoms;  
   double COMvel[3];
   double vel[3];
+  double zSysCOMVel;
 
-  double tempMass = 0;
-  double tempMVz =0;
-  double tempVz = 0;
-  for(int i = 0; i < nMols; i++){
-    molecules[i].getCOMvel(COMvel);
-    tempMass +=molecules[i].getTotalMass();  
- 	 tempMVz += molecules[i].getTotalMass() * COMvel[whichDirection];
-	 tempVz += COMvel[whichDirection];
-  }
-  cout << "initial velocity of center of mass is " << tempMVz / tempMass << endl;
-
   //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){	
+    if (states[i] == zcsFixed){ 
 
-	   zconsMols[i]->getCOMvel(COMvel);      
-		cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
+     zconsMols[i]->getCOMvel(COMvel);      
+     //cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
 
       fixedZAtoms = zconsMols[i]->getMyAtoms(); 
-	  
+    
       for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
         fixedZAtoms[j]->getVel(vel);
-	     vel[whichDirection] -= COMvel[whichDirection];
-	     fixedZAtoms[j]->setVel(vel);
+       vel[whichDirection] -= COMvel[whichDirection];
+       fixedZAtoms[j]->setVel(vel);
       }
 
-		zconsMols[i]->getCOMvel(COMvel);
-		cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
+    zconsMols[i]->getCOMvel(COMvel);
+    //cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
     }
-	
+  
   }
 
-  	cout << "before resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;	
-		   
+    //cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; 
+
+  zSysCOMVel = calcSysCOMVel();
+#ifdef IS_MPI
+  if(worldRank == 0){
+#endif
+     //cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;  
+#ifdef IS_MPI
+  }
+#endif
+       
   // calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
   double MVzOfMovingMols_local;
   double MVzOfMovingMols;
@@ -602,18 +695,18 @@ 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];   
-      totalMassOfMovingZMols_local += massOfZConsMols[i]; 	  	
+      totalMassOfMovingZMols_local += massOfZConsMols[i];       
     }
-		
+    
   }
 
 #ifndef IS_MPI
@@ -629,7 +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++){
@@ -642,48 +735,59 @@ 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){
    
       movingZAtoms = zconsMols[i]->getMyAtoms();
-	   for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
+     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
         movingZAtoms[j]->getVel(vel);
         vel[whichDirection] -= vzOfMovingMols;
-	     movingZAtoms[j]->setVel(vel);
-	  }
-	  
+       movingZAtoms[j]->setVel(vel);
+    }
+    
    }
 
  }
 
-	cout << "after resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
 
+  zSysCOMVel = calcSysCOMVel();
+#ifdef IS_MPI
+  if(worldRank == 0){
+#endif
+     //cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;  
+#ifdef IS_MPI
+  }
+#endif
+
 }
 
+/**
+ * 
+ */
+
 template<typename T> void ZConstraint<T>::doZconstraintForce(){
 
   Atom** zconsAtoms;
   double totalFZ; 
   double totalFZ_local;
-  double COMvel[3];   
   double COM[3];
   double force[3];
 
-  int nMovingZMols_local;
-  int nMovingZMols;
-
-  //constrain the molecules which do not reach the specified positions	
+  //constrain the molecules which do not reach the specified positions  
     
   //Zero Out the force of z-contrained molecules    
   totalFZ_local = 0;
 
   //calculate the total z-contrained force of fixed z-contrained molecules
-  cout << "Fixed Molecules" << endl;
-  for(int i = 0; i < zconsMols.size(); i++){
-		
+  
+  //cout << "before zero out z-constraint force on fixed z-constraint molecuels "
+  //       << "total force is " << calcTotalForce() << endl;
+
+  for(int i = 0; i < (int)(zconsMols.size()); i++){
+    
     if (states[i] == zcsFixed){
-	  	
+      
       zconsMols[i]->getCOM(COM);
       zconsAtoms = zconsMols[i]->getMyAtoms();  
 
@@ -691,126 +795,88 @@ template<typename T> void ZConstraint<T>::doZconstrain
       for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
         zconsAtoms[j]->getFrc(force);
         fz[i] += force[whichDirection];      
-      }	
+      } 
       totalFZ_local += fz[i];
 
-      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
+      //cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] 
+      //      <<"\tcurrent zpos: " << COM[whichDirection] 
+      //      << "\tcurrent fz: " <<fz[i] << endl;
 
+
     }
-	  
+    
   } 
 
-  //calculate the number of atoms of moving z-constrained molecules
-  nMovingZMols_local = 0;
-  for(int i = 0; i < zconsMols.size(); i++)
-    if(states[i] == zcsMoving)
-	   nMovingZMols_local += massOfZConsMols[i];
-  
+  //calculate total z-constraint force
 #ifdef IS_MPI
   MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
-  MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
 #else
   totalFZ = totalFZ_local;
-  nMovingZMols = nMovingZMols_local;
 #endif
 
-  force[0]= 0;
-  force[1]= 0;
-  force[2]= 0;
-  force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
-
-  //modify the forces of unconstrained molecules
-  for(int i = 0; i < unconsMols.size(); i++){
-     
-     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
-     
-     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
-       unconsAtoms[j]->addFrc(force);
-     
-  }      
-
- //modify the forces of moving z-constrained molecules
-  for(int i = 0; i < zconsMols.size(); i++) {
-   if (states[i] == zcsMoving){
-	 	
-     Atom** movingZAtoms = zconsMols[i]->getMyAtoms();     
-
-     for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
-       movingZAtoms[j]->addFrc(force);
-     }
-  }
-
+  
   // apply negative to fixed z-constrained molecues;
   force[0]= 0;
   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){  
-	
+  
       int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
       zconsAtoms = zconsMols[i]->getMyAtoms();  
     
       for(int j =0; j < nAtomOfCurZConsMol; j++) {
-        force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
+        //force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
+        force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]);
         zconsAtoms[j]->addFrc(force);
       }
-		
+    
     }
-	
+  
   } 
 
-}
+  //cout << "after zero out z-constraint force on fixed z-constraint molecuels "
+  //      << "total force is " << calcTotalForce() << endl;
+   
 
-template<typename T> bool ZConstraint<T>::checkZConsState(){
-  double COM[3];
-  double diff;
-  
-  bool changed;
-  
-  changed = false;
-  
-  for(int i =0; i < zconsMols.size(); i++){
+  force[0]= 0;
+  force[1]= 0;
+  force[2]= 0;
 
-    zconsMols[i]->getCOM(COM);
-    diff = fabs(COM[whichDirection] - zPos[i]);  
-    if (  diff <= zconsTol && states[i] == zcsMoving){
-      states[i] = zcsFixed;
-	changed = true;
+  //modify the forces of unconstrained molecules
+  for(int i = 0; i < (int)(unconsMols.size()); i++){
+     
+     Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
+     
+     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
+       //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
+       force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ);
+       unconsAtoms[j]->addFrc(force);
+     }
+     
+  }      
+
+ //modify the forces of moving z-constrained molecules
+  for(int i = 0; i < (int)(zconsMols.size()); i++) {
+    if (states[i] == zcsMoving){
+    
+      Atom** movingZAtoms = zconsMols[i]->getMyAtoms();     
+
+      for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
+        //force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
+        force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ);
+        movingZAtoms[j]->addFrc(force);
+      }
     }
-    else if ( diff > zconsTol && states[i] == zcsFixed){
-      states[i] = zcsMoving;
-	changed = true;	  
-    }
-  
   }
+//  cout << "after substracting z-constraint force from moving molecuels "
+//        << "total force is " << calcTotalForce()  << endl;
 
-  return changed;
 }
 
-template<typename T> bool ZConstraint<T>::haveFixedZMols(){
-  for(int i = 0; i < zconsMols.size(); i++)
-    if (states[i] == zcsFixed)
-      return true;
-
-  return false;
-}
-
-
 /**
- *
- */
-template<typename T> bool ZConstraint<T>::haveMovingZMols(){
-  for(int i = 0; i < zconsMols.size(); i++)
-    if (states[i] == zcsMoving)
-      return true;
-
-  return false;
-  
-}
-
-/**
   * 
   *
   */
@@ -821,55 +887,165 @@ template<typename T> void ZConstraint<T>::doHarmonic()
   double harmonicF;
   double COM[3];
   double diff;
+  double totalFZ_local;
   double totalFZ;
-	
+  
   force[0] = 0;
   force[1] = 0;
   force[2] = 0;
 
-  totalFZ = 0;
+  totalFZ_local = 0;
 
-  cout << "Moving Molecules" << endl;	
-  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);
-      cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
-		
-		diff = COM[whichDirection] -zPos[i];
-		
+//       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] 
+// 	   << "\tcurrent zpos: " << COM[whichDirection] << endl;
+
+      diff = COM[whichDirection] -zPos[i];
+    
       harmonicU = 0.5 * kz[i] * diff * diff;  
-		info->lrPot += harmonicU;
+      info->lrPot += harmonicU;
 
-      harmonicF =  - kz[i] * diff / zconsMols[i]->getNAtoms();
-		force[whichDirection] = harmonicF;
-      totalFZ += harmonicF;
-		
+      harmonicF =  - kz[i] * diff;
+      totalFZ_local += harmonicF;
+
+       //adjust force
+    
       Atom** movingZAtoms = zconsMols[i]->getMyAtoms();     
 
-       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)          
+       for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){          
+        //force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
+        force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF);
          movingZAtoms[j]->addFrc(force);
+       }
     }
 
   }
 
+#ifndef IS_MPI
+  totalFZ = totalFZ_local;
+#else
+  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;
+
   force[0]= 0;
   force[1]= 0;
   force[2]= 0;
-  force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
 
   //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();
      
-     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)          
+     for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){          
+       //force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
+       force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ);
        unconsAtoms[j]->addFrc(force);     
+     }
   }   
 
+  //cout << "after substracting harmonic force from moving molecuels "
+  //      << "total force is " << calcTotalForce()  << endl;
+
 }
 
-template<typename T> double ZConstraint<T>::calcCOMVel()
+/**
+ * 
+ */
+
+template<typename T> bool ZConstraint<T>::checkZConsState(){
+  double COM[3];
+  double diff;
+  
+  int changed_local;
+  int changed;
+  
+  changed_local = 0;
+  
+  for(int i =0; i < (int)(zconsMols.size()); i++){
+
+    zconsMols[i]->getCOM(COM);
+    diff = fabs(COM[whichDirection] - zPos[i]);  
+    if (  diff <= zconsTol && states[i] == zcsMoving){
+      states[i] = zcsFixed;
+     changed_local = 1;
+    }
+    else if ( diff > zconsTol && states[i] == zcsFixed){
+      states[i] = zcsMoving;
+     changed_local = 1;   
+    }
+  
+  }
+
+#ifndef IS_MPI
+  changed =changed_local; 
+#else
+  MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+#endif
+
+  return (changed > 0);
+
+}
+
+template<typename T> bool ZConstraint<T>::haveFixedZMols(){
+
+  int havingFixed_local;
+  int havingFixed;
+
+  havingFixed_local = 0;
+
+  for(int i = 0; i < (int)(zconsMols.size()); i++)
+    if (states[i] == zcsFixed){
+      havingFixed_local = 1;
+    break;
+    }
+
+#ifndef IS_MPI
+  havingFixed = havingFixed_local;
+#else
+  MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+#endif
+
+  return (havingFixed > 0);
+}
+
+
+/**
+ *
+ */
+template<typename T> bool ZConstraint<T>::haveMovingZMols(){
+
+  int havingMoving_local;
+  int havingMoving;
+
+  havingMoving_local = 0;
+
+  for(int i = 0; i < (int)(zconsMols.size()); i++)
+    if (states[i] == zcsMoving){
+      havingMoving_local = 1;
+    break;
+    }
+
+#ifndef IS_MPI
+  havingMoving = havingMoving_local;
+#else
+  MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+#endif
+
+  return (havingMoving > 0);
+  
+}
+
+/**
+ *
+ */
+
+template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel()
 {
   double MVzOfMovingMols_local;
   double MVzOfMovingMols;
@@ -890,9 +1066,9 @@ template<typename T> double ZConstraint<T>::calcCOMVel
     if (states[i] == zcsMoving){
       zconsMols[i]->getCOMvel(COMvel);
       MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];   
-      totalMassOfMovingZMols_local += massOfZConsMols[i]; 	  	
+      totalMassOfMovingZMols_local += massOfZConsMols[i];       
     }
-		
+    
   }
 
 #ifndef IS_MPI
@@ -909,24 +1085,142 @@ template<typename T> double ZConstraint<T>::calcCOMVel
   return vzOfMovingMols;
 }
 
+/**
+ *
+ */
 
-template<typename T> double ZConstraint<T>::calcCOMVel2()
+template<typename T> double ZConstraint<T>::calcSysCOMVel()
 {
   double COMvel[3];
-  double tempMVz = 0;
-  int index;
-		
+  double tempMVz_local;
+  double tempMVz;
+  double massOfZCons_local;
+  double massOfZCons;
+
+
+ tempMVz_local = 0;
+
   for(int i =0 ; i < nMols; i++){
-	 index = isZConstraintMol(&molecules[i]);
-    if( index == -1){
-       molecules[i].getCOMvel(COMvel);
-	    tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
-    }
-	 else if(states[i] == zcsMoving){
-       zconsMols[index]->getCOMvel(COMvel);
-	    tempMVz += massOfZConsMols[index]*COMvel[whichDirection];    
-	 }
+    molecules[i].getCOMvel(COMvel);
+   tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection];
   }
-	
-  return tempMVz /totalMassOfUncons;
+
+  massOfZCons_local = 0;
+  
+  for(int i = 0; i < (int)(massOfZConsMols.size()); i++){
+    massOfZCons_local += massOfZConsMols[i];
+  }
+#ifndef IS_MPI
+  massOfZCons = massOfZCons_local;
+  tempMVz = tempMVz_local;
+#else
+  MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+  MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+#endif
+
+  return tempMVz /(totalMassOfUncons + massOfZCons);
 }
+
+/**
+ *
+ */
+
+template<typename T> double ZConstraint<T>::calcTotalForce(){
+
+  double force[3];  
+  double totalForce_local;
+  double totalForce;
+
+  totalForce_local = 0;
+
+  for(int i = 0; i < nAtoms; i++){
+    atoms[i]->getFrc(force);
+    totalForce_local += force[whichDirection];
+  }
+
+#ifndef IS_MPI
+  totalForce = totalForce_local;
+#else
+  MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+#endif
+
+  return totalForce;
+
+}
+
+/**
+ *
+ */
+
+template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
+  //calculate the number of atoms of moving z-constrained molecules
+  int nMovingZAtoms_local;
+  int nMovingZAtoms;
+  
+  nMovingZAtoms_local = 0;
+  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
+    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
+     nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
+  
+#ifdef IS_MPI
+  MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+#else
+  nMovingZAtoms = nMovingZAtoms_local;
+#endif
+  totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
+}
+
+template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
+  return totalForce / mol->getNAtoms();
+}
+
+template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){
+  return totalForce / totNumOfMovingAtoms;
+}
+
+template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
+    return totalForce / mol->getNAtoms();
+}
+
+template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){
+  return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
+}
+
+/**
+ *
+ */
+
+template<typename T> void ZConstraint<T>::PolicyByMass::update(){
+  //calculate the number of atoms of moving z-constrained molecules
+  double massOfMovingZAtoms_local;
+  double massOfMovingZAtoms;
+  
+  massOfMovingZAtoms_local = 0;
+  for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++)
+    if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving))
+     massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
+  
+#ifdef IS_MPI
+  MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
+#else
+  massOfMovingZAtoms = massOfMovingZAtoms_local;
+#endif
+  totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons;
+}
+
+template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
+  return totalForce * atom->getMass() / mol->getTotalMass();
+}
+
+template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){
+    return totalForce * atom->getMass() / totMassOfMovingAtoms;
+}
+
+template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){
+  return totalForce * atom->getMass() / mol->getTotalMass();
+}
+
+template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){
+    return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
+}
+