--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/08/11 19:40:06	676
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/08/13 19:21:53	693
@@ -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++){
@@ -1358,8 +1362,8 @@ void SimSetup::makeIntegrator( void ){
     switch( ensembleCase ){
       
     case NVE_ENS:
-	if (haveZConstraint){
-         setupZConstraint();
+	if (globals->haveZconstraints()){
+         setupZConstraint(info[k]);
 	   new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
 	}
 
@@ -1368,8 +1372,8 @@ void SimSetup::makeIntegrator( void ){
       break;
       
     case NVT_ENS:
-	if (haveZConstraint){
-         setupZConstraint();
+	if (globals->haveZconstraints()){
+         setupZConstraint(info[k]);
 	   myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
 	}
 	else
@@ -1390,8 +1394,8 @@ void SimSetup::makeIntegrator( void ){
       break;
       
     case NPTi_ENS:
-	if (haveZConstraint){
-         setupZConstraint();
+	if (globals->haveZconstraints()){
+         setupZConstraint(info[k]);
 	   myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
 	}
 	else
@@ -1431,8 +1435,8 @@ void SimSetup::makeIntegrator( void ){
       break;
       
     case NPTf_ENS:
-	if (haveZConstraint){
-         setupZConstraint();
+	if (globals->haveZconstraints()){
+         setupZConstraint(info[k]);
 	   myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
 	}
 	else
@@ -1472,8 +1476,8 @@ void SimSetup::makeIntegrator( void ){
       break;
       
     case NPTim_ENS:
-	if (haveZConstraint){
-         setupZConstraint();
+	if (globals->haveZconstraints()){
+         setupZConstraint(info[k]);
 	   myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
 	}
 	else
@@ -1513,8 +1517,8 @@ void SimSetup::makeIntegrator( void ){
       break;
       
     case NPTfm_ENS:
-	if (haveZConstraint){
-         setupZConstraint();
+	if (globals->haveZconstraints()){
+         setupZConstraint(info[k]);
 	   myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
 	}
 	else
@@ -1589,19 +1593,18 @@ void SimSetup::initFortran( void ){
 
 }
 
-void SimSetup::setupZConstraint()
+void SimSetup::setupZConstraint(SimInfo& theInfo)
 {
-  int k;
-
-  for(k=0; k<nInfo; k++){
-    
-    if(globals->haveZConsTime()){   
+    int nZConstraints;
+    ZconStamp** zconStamp;
+	
+    if(globals->haveZconstraintTime()){   
       
       //add sample time of z-constraint  into SimInfo's property list                    
       DoubleData* zconsTimeProp = new DoubleData();
-      zconsTimeProp->setID("zconstime");
-      zconsTimeProp->setData(globals->getZConsTime());
-      info[k].addProperty(zconsTimeProp);
+      zconsTimeProp->setID(ZCONSTIME_ID);
+      zconsTimeProp->setData(globals->getZconsTime());
+      theInfo.addProperty(zconsTimeProp);
     }
     else{
       sprintf( painCave.errMsg,
@@ -1610,41 +1613,62 @@ void SimSetup::setupZConstraint()
       painCave.isFatal = 1;
       simError();      
     }
-    
-    if(globals->haveIndexOfAllZConsMols()){
- 
-      //add index of z-constraint molecules into SimInfo's property list
-      vector<int> tempIndex = globals->getIndexOfAllZConsMols();
-      
-      //sort the index
-      sort(tempIndex.begin(), tempIndex.end());
-      
-      IndexData* zconsIndex = new IndexData();
-      zconsIndex->setID("zconsindex");
-      zconsIndex->setIndexData(tempIndex);
-      info[k].addProperty(zconsIndex);
+
+    //
+    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);
     }
-    else{
-      sprintf( painCave.errMsg,
-	       "SimSetup error: If you use an ZConstraint\n"
-	       " , you must set index of z-constraint molecules.\n");
-      painCave.isFatal = 1;
-      simError();     
-      
+
+    //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();
+    zconsTol->setID(ZCONSTOL_ID);
+    if(globals->haveZconsTol()){
+      zconsTol->setData(globals->getZconsTol());
     }
-    
+	 else{
+	 	double defaultZConsTol = 1E-6;
+      sprintf( painCave.errMsg,
+	       "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
+	       " , default value %f is used.\n", defaultZConsTol);
+      painCave.isFatal = 0;
+      simError();      
+
+      zconsTol->setData(defaultZConsTol);
+	 }
+    theInfo.addProperty(zconsTol);
+	 
     //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
     
-    string zconsOutput(info[k].finalName);
+    string zconsOutput(theInfo.finalName);
     
     zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
     
     StringData* zconsFilename = new StringData();
-    zconsFilename->setID("zconsfilename");
+    zconsFilename->setID(ZCONSFILENAME_ID);
     zconsFilename->setData(zconsOutput);
     
-    info[k].addProperty(zconsFilename);      
-  }
+    theInfo.addProperty(zconsFilename);      
 }