--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/08/12 19:56:49	689
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/08/15 19:24:13	699
@@ -98,25 +98,17 @@ void SimSetup::createSim(void){
   
   // gather all of the information from the Bass file
 
-  std::cerr << "gathering info\n";
-
   gatherInfo();
 
   // creation of complex system objects
 
-  std::cerr << "creating system objects\n";
-
   sysObjectsCreation();
 
   // check on the post processing info
-  
-  std::cerr << "performing final info check.\n";
 
   finalInfoCheck();
 
   // initialize the system coordinates
-
-  std::cerr << "about to init coords\n";
 
   if( !isInfoArray ) initSystemCoords();  
 
@@ -899,7 +891,6 @@ void SimSetup::initSystemCoords( void ){
   
   char* inName;
 
-  std::cerr << "Setting atom Coords\n";
 
   (info[0].getConfiguration())->createArrays( info[0].n_atoms );
   
@@ -912,6 +903,7 @@ void SimSetup::initSystemCoords( void ){
     if( worldRank == 0 ){
 #endif //is_mpi
       inName = globals->getInitialConfig();
+      double* tempDouble = new double[1000000];
       fileInit = new InitializeFromFile( inName );
 #ifdef IS_MPI
     }else fileInit = new InitializeFromFile( NULL );
@@ -1620,31 +1612,8 @@ void SimSetup::setupZConstraint(SimInfo& theInfo)
 	       " , you must set sample time.\n");
       painCave.isFatal = 1;
       simError();      
-    }
-
-    //
-    nZConstraints = globals->getNzConstraints();
-    zconStamp = globals->getZconStamp();
-    ZConsParaItem tempParaItem;
-
-    ZConsParaData* zconsParaData = new ZConsParaData();
-    zconsParaData->setID(ZCONSPARADATA_ID);
-   
-    for(int i = 0; i < nZConstraints; i++){
-    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
-    tempParaItem.zPos = zconStamp[i]->getZpos();
-    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
-    tempParaItem.kRatio = zconStamp[i]->getKratio();
-
-    zconsParaData->addItem(tempParaItem);
     }
 
-    //sort the parameters by index of molecules
-    zconsParaData->sortByIndex();
-	
-    //push data into siminfo, therefore, we can retrieve later
-    theInfo.addProperty(zconsParaData);
-
     //push zconsTol into siminfo, if user does not specify
     //value for zconsTol, a default value will be used
     DoubleData* zconsTol = new DoubleData();
@@ -1653,7 +1622,7 @@ void SimSetup::setupZConstraint(SimInfo& theInfo)
       zconsTol->setData(globals->getZconsTol());
     }
 	 else{
-	 	double defaultZConsTol = 1E-6;
+	 	double defaultZConsTol = 0.01;
       sprintf( painCave.errMsg,
 	       "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
 	       " , default value %f is used.\n", defaultZConsTol);
@@ -1663,7 +1632,25 @@ void SimSetup::setupZConstraint(SimInfo& theInfo)
       zconsTol->setData(defaultZConsTol);
 	 }
     theInfo.addProperty(zconsTol);
+
+    //set Force Substraction Policy
+    StringData* zconsForcePolicy =  new StringData();
+    zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
+		
+	 if(globals->haveZconsForcePolicy()){
+      zconsForcePolicy->setData(globals->getZconsForcePolicy());
+	 }	
+	 else{
+       sprintf( painCave.errMsg,
+               "ZConstraint Warning: User does not set force substraction policy, "
+               "average force substraction policy is used\n");
+       painCave.isFatal = 0;
+       simError(); 
+		 zconsForcePolicy->setData("BYNUMBER");
+	 }
 	 
+	 theInfo.addProperty(zconsForcePolicy);
+	 
     //Determine the name of ouput file and add it into SimInfo's property list 
     //Be careful, do not use inFileName, since it is a pointer which
     //point to a string at master node, and slave nodes do not contain that string
@@ -1676,5 +1663,31 @@ void SimSetup::setupZConstraint(SimInfo& theInfo)
     zconsFilename->setID(ZCONSFILENAME_ID);
     zconsFilename->setData(zconsOutput);
     
-    theInfo.addProperty(zconsFilename);      
+    theInfo.addProperty(zconsFilename);
+		
+    //setup index, pos and other parameters of z-constraint molecules
+    nZConstraints = globals->getNzConstraints();
+    theInfo.nZconstraints = nZConstraints;
+	
+    zconStamp = globals->getZconStamp();
+    ZConsParaItem tempParaItem;
+
+    ZConsParaData* zconsParaData = new ZConsParaData();
+    zconsParaData->setID(ZCONSPARADATA_ID);
+   
+    for(int i = 0; i < nZConstraints; i++){
+    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
+    tempParaItem.zPos = zconStamp[i]->getZpos();
+    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
+    tempParaItem.kRatio = zconStamp[i]->getKratio();
+
+    zconsParaData->addItem(tempParaItem);
+    }
+
+    //sort the parameters by index of molecules
+    zconsParaData->sortByIndex();
+	
+    //push data into siminfo, therefore, we can retrieve later
+    theInfo.addProperty(zconsParaData);
+      
 }