--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/07/16 02:11:02	621
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/07/29 16:32:37	656
@@ -24,12 +24,17 @@
 
 #define FF_DUFF 0
 #define FF_LJ   1
+#define FF_EAM  2
 
-
 SimSetup::SimSetup(){
+  
+  isInfoArray = 0;
+  nInfo = 1;
+  
   stamps = new MakeStamps();
   globals = new Globals();
   
+  
 #ifdef IS_MPI
   strcpy( checkPointMsg, "SimSetup creation successful" );
   MPIcheckPoint();
@@ -40,7 +45,14 @@ SimSetup::~SimSetup(){
   delete stamps;
   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 +598,7 @@ 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",
@@ -762,6 +775,7 @@ void SimSetup::finalInfoCheck( void ){
   MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
 #endif //is_mpi
 
+  double theEcr, theEst;
 
   if (globals->getUseRF() ) {
     info->useReactionField = 1;
@@ -777,9 +791,9 @@ void SimSetup::finalInfoCheck( void ){
       smallest = info->boxL[0];
       if (info->boxL[1] <= smallest) smallest = info->boxL[1];
       if (info->boxL[2] <= smallest) smallest = info->boxL[2];
-      info->ecr = 0.5 * smallest;
+      theEcr = 0.5 * smallest;
     } else {
-      info->ecr        = globals->getECR();
+      theEcr = globals->getECR();
     }
 
     if( !globals->haveEST() ){
@@ -789,10 +803,12 @@ void SimSetup::finalInfoCheck( void ){
                );
       painCave.isFatal = 0;
       simError();
-      info->est = 0.05 * info->ecr;
+      theEst = 0.05 * theEcr;
     } else {
-      info->est        = globals->getEST();
+      theEst= globals->getEST();
     }
+
+    info->setEcr( theEcr, theEst );
     
     if(!globals->haveDielectric() ){
       sprintf( painCave.errMsg,
@@ -808,33 +824,35 @@ void SimSetup::finalInfoCheck( void ){
     if (usesDipoles) {
       
       if( !globals->haveECR() ){
-        sprintf( painCave.errMsg,
-                 "SimSetup Warning: using default value of 1/2 the smallest "
-                 "box length for the electrostaticCutoffRadius.\n"
-                 "I hope you have a very fast processor!\n");
-        painCave.isFatal = 0;
-        simError();
-        double smallest;
-        smallest = info->boxL[0];
-        if (info->boxL[1] <= smallest) smallest = info->boxL[1];
-        if (info->boxL[2] <= smallest) smallest = info->boxL[2];
-        info->ecr = 0.5 * smallest;
+	sprintf( painCave.errMsg,
+		 "SimSetup Warning: using default value of 1/2 the smallest "
+		 "box length for the electrostaticCutoffRadius.\n"
+		 "I hope you have a very fast processor!\n");
+	painCave.isFatal = 0;
+	simError();
+	double smallest;
+	smallest = info->boxL[0];
+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
+	theEcr = 0.5 * smallest;
       } else {
-        info->ecr        = globals->getECR();
+	theEcr = globals->getECR();
       }
       
       if( !globals->haveEST() ){
-        sprintf( painCave.errMsg,
-                 "SimSetup Warning: using default value of 5%% of the "
-                 "electrostaticCutoffRadius for the "
-                 "electrostaticSkinThickness\n"
-                 );
-        painCave.isFatal = 0;
-        simError();
-        info->est = 0.05 * info->ecr;
+	sprintf( painCave.errMsg,
+		 "SimSetup Warning: using default value of 0.05 * the "
+		 "electrostaticCutoffRadius for the "
+		 "electrostaticSkinThickness\n"
+		 );
+	painCave.isFatal = 0;
+	simError();
+	theEst = 0.05 * theEcr;
       } else {
-        info->est        = globals->getEST();
+	theEst= globals->getEST();
       }
+
+      info->setEcr( theEcr, theEst );
     }
   }  
 
@@ -857,7 +875,7 @@ 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;
  }
@@ -1025,6 +1043,10 @@ void SimSetup::createFF( void ){
 
   case FF_LJ:
     the_ff = new LJFF();
+    break;
+
+  case FF_EAM:
+    the_ff = new EAM_FF();
     break;
 
   default:
@@ -1276,20 +1298,20 @@ 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;
 
   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()) 
@@ -1305,7 +1327,7 @@ 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())
@@ -1340,7 +1362,7 @@ 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())
@@ -1375,7 +1397,7 @@ 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())
@@ -1410,7 +1432,7 @@ 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())