--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/08/12 17:51:33	682
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/08/15 19:24:13	699
@@ -5,6 +5,7 @@
 #include <string>
 
 #include "SimSetup.hpp"
+#include "ReadWrite.hpp"
 #include "parse_me.h"
 #include "Integrator.hpp"
 #include "simError.h"
@@ -96,7 +97,7 @@ void SimSetup::createSim(void){
   int i, j, k, globalAtomIndex;
   
   // gather all of the information from the Bass file
-  
+
   gatherInfo();
 
   // creation of complex system objects
@@ -104,7 +105,7 @@ void SimSetup::createSim(void){
   sysObjectsCreation();
 
   // check on the post processing info
-  
+
   finalInfoCheck();
 
   // initialize the system coordinates
@@ -888,8 +889,9 @@ void SimSetup::initSystemCoords( void ){
 void SimSetup::initSystemCoords( void ){
   int i;
   
-  std::cerr << "Setting atom Coords\n";
+  char* inName;
 
+
   (info[0].getConfiguration())->createArrays( info[0].n_atoms );
   
   for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
@@ -900,7 +902,9 @@ void SimSetup::initSystemCoords( void ){
 #ifdef IS_MPI // is_mpi
     if( worldRank == 0 ){
 #endif //is_mpi
-      fileInit = new InitializeFromFile( globals->getInitialConfig() );
+      inName = globals->getInitialConfig();
+      double* tempDouble = new double[1000000];
+      fileInit = new InitializeFromFile( inName );
 #ifdef IS_MPI
     }else fileInit = new InitializeFromFile( NULL );
 #endif
@@ -1033,7 +1037,7 @@ void SimSetup::sysObjectsCreation( void ){
   int i,k;
   
   // create the forceField
-  
+
   createFF();
 
   // extract componentList
@@ -1051,11 +1055,11 @@ void SimSetup::sysObjectsCreation( void ){
 #endif //is_mpi
   
   // create the atom and SRI arrays. Also initialize Molecule Stamp ID's
-  
+ 
   makeSysArrays();
 
   // make and initialize the molecules (all but atomic coordinates)
-  
+ 
   makeMolecules();
   
   for(k=0; k<nInfo; k++){
@@ -1608,31 +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();
@@ -1641,7 +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);
@@ -1651,7 +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
@@ -1664,5 +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);
+      
 }