--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/06/19 19:11:53	557
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/07/02 21:26:55	572
@@ -97,7 +97,7 @@ void SimSetup::createSim( void ){
   n_components = the_globals->getNComponents();
   strcpy( force_field, the_globals->getForceField() );
 
-  if( !strcasecmp( force_field, "DUFF" ))    ffCase = FF_DUFF;
+  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
   else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
   else{
     sprintf( painCave.errMsg,
@@ -110,9 +110,9 @@ void SimSetup::createSim( void ){
   // get the ensemble:
   strcpy( ensemble, the_globals->getEnsemble() );
 
-  if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
-  else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
-  else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
+  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
+  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
+  else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
   else{
     sprintf( painCave.errMsg,
 	     "SimSetup Warning. Unrecognized Ensemble -> %s, "
@@ -193,7 +193,7 @@ void SimSetup::createSim( void ){
     break;
 
   case FF_LJ:
-    the_ff = LJFF();
+    the_ff = new LJFF();
     break;
 
   default:
@@ -479,19 +479,23 @@ void SimSetup::createSim( void ){
 
   // get some of the tricky things that may still be in the globals
 
-  
+  double boxVector[3];
   if( the_globals->haveBox() ){
-    simnfo->box_x = the_globals->getBox();
-    simnfo->box_y = the_globals->getBox();
-    simnfo->box_z = the_globals->getBox();
+    boxVector[0] = the_globals->getBox();
+    boxVector[1] = the_globals->getBox();
+    boxVector[2] = the_globals->getBox();
+    
+    simnfo->setBox( boxVector );
   }
   else if( the_globals->haveDensity() ){
 
     double vol;
     vol = (double)tot_nmol / the_globals->getDensity();
-    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
-    simnfo->box_y = simnfo->box_x;
-    simnfo->box_z = simnfo->box_x;
+     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
+     boxVector[1] = boxVector[0];
+     boxVector[2] = boxVector[0];
+
+    simnfo->setBox( boxVector );
   }
   else{
     if( !the_globals->haveBoxX() ){
@@ -500,7 +504,7 @@ void SimSetup::createSim( void ){
       painCave.isFatal = 1;
       simError();
     }
-    simnfo->box_x = the_globals->getBoxX();
+    boxVector[0] = the_globals->getBoxX();
 
     if( !the_globals->haveBoxY() ){
       sprintf( painCave.errMsg,
@@ -508,7 +512,7 @@ void SimSetup::createSim( void ){
       painCave.isFatal = 1;
       simError();
     }
-    simnfo->box_y = the_globals->getBoxY();
+    boxVector[1] = the_globals->getBoxY();
 
     if( !the_globals->haveBoxZ() ){
       sprintf( painCave.errMsg,
@@ -516,7 +520,9 @@ void SimSetup::createSim( void ){
       painCave.isFatal = 1;
       simError();
     }
-    simnfo->box_z = the_globals->getBoxZ();
+    boxVector[2] = the_globals->getBoxZ();
+
+    simnfo->setBox( boxVector );
   }
 
 #ifdef IS_MPI
@@ -546,9 +552,9 @@ void SimSetup::createSim( void ){
       painCave.isFatal = 0;
       simError();
       double smallest;
-      smallest = simnfo->box_x;
-      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
-      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
+      smallest = simnfo->boxLx;
+      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
+      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
       simnfo->ecr = 0.5 * smallest;
     } else {
       simnfo->ecr        = the_globals->getECR();
@@ -586,9 +592,9 @@ void SimSetup::createSim( void ){
         painCave.isFatal = 0;
         simError();
         double smallest;
-        smallest = simnfo->box_x;
-        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
-        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
+        smallest = simnfo->boxLx;
+        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
+        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
         simnfo->ecr = 0.5 * smallest;
       } else {
         simnfo->ecr        = the_globals->getECR();
@@ -768,15 +774,41 @@ void SimSetup::createSim( void ){
 
 
   // make the integrator
+  
+  
+  NVT* myNVT = NULL;
+  switch( ensembleCase ){
 
+  case NVE_ENS:
+    new NVE( simnfo, the_ff );
+    break;
 
-  if( !strcmp( ensemble, "TraPPE_Ex" ) ){
-    new Symplectic(simnfo, the_ff, the_extendedsystem);
-  }
-  else if( !strcmp( force_field, "LJ" ) ){
-    new Verlet( *simnfo, the_ff, the_extendedsystem );
+  case NVT_ENS:
+    myNVT = new NVT( simnfo, the_ff );
+    myNVT->setTargetTemp(the_globals->getTargetTemp());
+
+    if (the_globals->haveTauThermostat()) 
+      myNVT->setTauThermostat(the_globals->getTauThermostat());
+//     else if (the_globals->haveQmass())
+//       myNVT->setQmass(the_globals->getQmass());
+    else {
+      sprintf( painCave.errMsg,
+               "SimSetup error: If you use the NVT\n"
+               "    ensemble, you must set either tauThermostat or qMass.\n"
+               "    Neither of these was found in the BASS file.\n");
+      painCave.isFatal = 1;
+      simError();
+    }
+    break;
+
+  default:
+    sprintf( painCave.errMsg,
+	     "SimSetup Error. Unrecognized ensemble in case statement.\n");
+    painCave.isFatal = 1;
+    simError();
   }
 
+
 #ifdef IS_MPI
   mpiSim->mpiRefresh();
 #endif
@@ -1089,9 +1121,9 @@ void SimSetup::initFromBass( void ){
     have_extra =1;
 
     n_cells = (int)temp3 - 1;
-    cellx = simnfo->box_x / temp3;
-    celly = simnfo->box_y / temp3;
-    cellz = simnfo->box_z / temp3;
+    cellx = simnfo->boxLx / temp3;
+    celly = simnfo->boxLy / temp3;
+    cellz = simnfo->boxLz / temp3;
     n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
     temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
     n_per_extra = (int)ceil( temp1 );
@@ -1106,9 +1138,9 @@ void SimSetup::initFromBass( void ){
   }
   else{
     n_cells = (int)temp3;
-    cellx = simnfo->box_x / temp3;
-    celly = simnfo->box_y / temp3;
-    cellz = simnfo->box_z / temp3;
+    cellx = simnfo->boxLx / temp3;
+    celly = simnfo->boxLy / temp3;
+    cellz = simnfo->boxLz / temp3;
   }
 
   current_mol = 0;