--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/07/16 21:30:56	626
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/07/31 15:35:07	658
@@ -1,6 +1,8 @@
+#include <algorithm>
 #include <cstdlib>
 #include <iostream>
 #include <cmath>
+#include <string>
 
 #include "SimSetup.hpp"
 #include "parse_me.h"
@@ -20,16 +22,24 @@
 #define NPTf_ENS  3
 #define NPTim_ENS 4
 #define NPTfm_ENS 5
+#define NVEZCONS_ENS 6
 
 
 #define FF_DUFF 0
 #define FF_LJ   1
+#define FF_EAM  2
 
+using namespace std;
 
 SimSetup::SimSetup(){
+  
+  isInfoArray = 0;
+  nInfo = 1;
+  
   stamps = new MakeStamps();
   globals = new Globals();
   
+  
 #ifdef IS_MPI
   strcpy( checkPointMsg, "SimSetup creation successful" );
   MPIcheckPoint();
@@ -41,6 +51,13 @@ SimSetup::~SimSetup(){
   delete globals;
 }
 
+void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
+    info = the_info;
+    nInfo = theNinfo;
+    isInfoArray = 1;
+  }
+
+
 void SimSetup::parseFile( char* fileName ){
 
 #ifdef IS_MPI
@@ -586,6 +603,7 @@ void SimSetup::gatherInfo( void ){
 
   if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
   else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
+  else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
   else{
     sprintf( painCave.errMsg,
 	     "SimSetup Error. Unrecognized force field -> %s\n",
@@ -605,6 +623,7 @@ void SimSetup::gatherInfo( void ){
   else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
   else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
   else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
+  else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
   else{
     sprintf( painCave.errMsg,
 	     "SimSetup Warning. Unrecognized Ensemble -> %s, "
@@ -862,7 +881,7 @@ void SimSetup::initSystemCoords( void ){
 #ifdef IS_MPI
      }else fileInit = new InitializeFromFile( NULL );
 #endif
-   fileInit->read_xyz( info ); // default velocities on
+   fileInit->readInit( info ); // default velocities on
 
    delete fileInit;
  }
@@ -1032,6 +1051,10 @@ void SimSetup::createFF( void ){
     the_ff = new LJFF();
     break;
 
+  case FF_EAM:
+    the_ff = new EAM_FF();
+    break;
+
   default:
     sprintf( painCave.errMsg,
 	     "SimSetup Error. Unrecognized force field in case statement.\n");
@@ -1281,20 +1304,23 @@ void SimSetup::makeIntegrator( void ){
 
 void SimSetup::makeIntegrator( void ){
 
-  NVT*  myNVT = NULL;
-  NPTi* myNPTi = NULL;
-  NPTf* myNPTf = NULL;
-  NPTim* myNPTim = NULL;
-  NPTfm* myNPTfm = NULL;
-
+  NVT<RealIntegrator>*  myNVT = NULL;
+  NPTi<RealIntegrator>* myNPTi = NULL;
+  NPTf<RealIntegrator>* myNPTf = NULL;
+  NPTim<RealIntegrator>* myNPTim = NULL;
+  NPTfm<RealIntegrator>* myNPTfm = NULL;
+  ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
+      
+  cerr << "setting integrator" <<endl;    
+  
   switch( ensembleCase ){
 
   case NVE_ENS:
-    new NVE( info, the_ff );
+    new NVE<RealIntegrator>( info, the_ff );
     break;
 
   case NVT_ENS:
-    myNVT = new NVT( info, the_ff );
+    myNVT = new NVT<RealIntegrator>( info, the_ff );
     myNVT->setTargetTemp(globals->getTargetTemp());
 
     if (globals->haveTauThermostat()) 
@@ -1310,7 +1336,7 @@ void SimSetup::makeIntegrator( void ){
     break;
 
   case NPTi_ENS:
-    myNPTi = new NPTi( info, the_ff );
+    myNPTi = new NPTi<RealIntegrator>( info, the_ff );
     myNPTi->setTargetTemp( globals->getTargetTemp() );
 
     if (globals->haveTargetPressure())
@@ -1345,7 +1371,7 @@ void SimSetup::makeIntegrator( void ){
     break;
 
   case NPTf_ENS:
-    myNPTf = new NPTf( info, the_ff );
+    myNPTf = new NPTf<RealIntegrator>( info, the_ff );
     myNPTf->setTargetTemp( globals->getTargetTemp());
 
     if (globals->haveTargetPressure())
@@ -1380,7 +1406,7 @@ void SimSetup::makeIntegrator( void ){
     break;
     
   case NPTim_ENS:
-    myNPTim = new NPTim( info, the_ff );
+    myNPTim = new NPTim<RealIntegrator>( info, the_ff );
     myNPTim->setTargetTemp( globals->getTargetTemp());
 
     if (globals->haveTargetPressure())
@@ -1415,7 +1441,7 @@ void SimSetup::makeIntegrator( void ){
     break;
 
   case NPTfm_ENS:
-    myNPTfm = new NPTfm( info, the_ff );
+    myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
     myNPTfm->setTargetTemp( globals->getTargetTemp());
 
     if (globals->haveTargetPressure())
@@ -1448,7 +1474,65 @@ void SimSetup::makeIntegrator( void ){
       simError();
     }
     break;
+    
+  case NVEZCONS_ENS:
+    {
+
+      if(globals->haveZConsTime()){   
+ 
+        //add sample time of z-constraint  into SimInfo's property list                    
+        DoubleData* zconsTimeProp = new DoubleData();
+        zconsTimeProp->setID("zconstime");
+        zconsTimeProp->setData(globals->getZConsTime());
+        info->addProperty(zconsTimeProp);
+      }
+      else{
+        sprintf( painCave.errMsg,
+                 "ZConstraint error: If you use an ZConstraint\n"
+                 " , you must set sample time.\n");
+        painCave.isFatal = 1;
+        simError();      
+      }
+      
+      if(globals->haveIndexOfAllZConsMols()){
+ 
+        //add index of z-constraint molecules into SimInfo's property list
+	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
+	sort(tempIndex.begin(), tempIndex.end());
+	
+        IndexData* zconsIndex = new IndexData();
+        zconsIndex->setID("zconsindex");
+        zconsIndex->setIndexData(tempIndex);
+        info->addProperty(zconsIndex);
+      }
+      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();     
+      
+      }
 
+      //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->finalName);
+            
+      zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
+                 
+      StringData* zconsFilename = new StringData();
+      zconsFilename->setID("zconsfilename");
+      zconsFilename->setData(zconsOutput);
+
+      info->addProperty(zconsFilename);      
+      
+      myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
+        
+    break;
+    }
+    
   default:
     sprintf( painCave.errMsg,
 	     "SimSetup Error. Unrecognized ensemble in case statement.\n");