--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/10/27 22:07:48	823
+++ branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp	2003/10/31 21:06:47	849
@@ -1,7 +1,7 @@
 #include <algorithm>
-#include <cstdlib>
+#include <stdlib.h>
 #include <iostream>
-#include <cmath>
+#include <math.h>
 #include <string>
 #include <sprng.h> 
 #include "SimSetup.hpp"
@@ -102,10 +102,6 @@ void SimSetup::createSim(void){
   // creation of complex system objects
 
   sysObjectsCreation();
-
-  // check on the post processing info
-
-  finalInfoCheck();
 
   // initialize the system coordinates
 
@@ -115,6 +111,10 @@ void SimSetup::createSim(void){
     if( !(globals->getUseInitTime()) )
       info[0].currentTime = 0.0;
   }  
+
+  // check on the post processing info
+
+  finalInfoCheck();
 
   // make the output filenames
 
@@ -696,58 +696,12 @@ void SimSetup::gatherInfo(void){
     }
 
     // check for the temperature set flag
-
+    
     if (globals->haveTempSet())
       info[i].setTemp = globals->getTempSet();
-
-    // get some of the tricky things that may still be in the globals
-
-    double boxVector[3];
-    if (globals->haveBox()){
-      boxVector[0] = globals->getBox();
-      boxVector[1] = globals->getBox();
-      boxVector[2] = globals->getBox();
-
-      info[i].setBox(boxVector);
-    }
-    else if (globals->haveDensity()){
-      double vol;
-      vol = (double) tot_nmol / globals->getDensity();
-      boxVector[0] = pow(vol, (1.0 / 3.0));
-      boxVector[1] = boxVector[0];
-      boxVector[2] = boxVector[0];
-
-      info[i].setBox(boxVector);
-    }
-    else{
-      if (!globals->haveBoxX()){
-        sprintf(painCave.errMsg,
-                "SimSetup error, no periodic BoxX size given.\n");
-        painCave.isFatal = 1;
-        simError();
-      }
-      boxVector[0] = globals->getBoxX();
-
-      if (!globals->haveBoxY()){
-        sprintf(painCave.errMsg,
-                "SimSetup error, no periodic BoxY size given.\n");
-        painCave.isFatal = 1;
-        simError();
-      }
-      boxVector[1] = globals->getBoxY();
-
-      if (!globals->haveBoxZ()){
-        sprintf(painCave.errMsg,
-                "SimSetup error, no periodic BoxZ size given.\n");
-        painCave.isFatal = 1;
-        simError();
-      }
-      boxVector[2] = globals->getBoxZ();
-
-      info[i].setBox(boxVector);
-    }
+    
   }
-
+  
   //setup seed for random number generator
   int seedValue;
 
@@ -851,7 +805,7 @@ void SimSetup::finalInfoCheck(void){
         theEst = globals->getEST();
       }
 
-      info[i].setEcr(theEcr, theEst);
+      info[i].setDefaultEcr(theEcr, theEst);
 
       if (!globals->haveDielectric()){
         sprintf(painCave.errMsg,
@@ -896,9 +850,10 @@ void SimSetup::finalInfoCheck(void){
           theEst = globals->getEST();
         }
 
-        info[i].setEcr(theEcr, theEst);
+        info[i].setDefaultEcr(theEcr, theEst);
       }
     }
+    info[i].checkCutOffs();
   }
 
 #ifdef IS_MPI
@@ -1352,31 +1307,38 @@ void SimSetup::makeIntegrator(void){
 void SimSetup::makeIntegrator(void){
   int k;
 
-  NVE<RealIntegrator>* myNVE = NULL;
-  NVT<RealIntegrator>* myNVT = NULL;
-  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
-  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
-  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
+  NVE* myNVE = NULL;
+  NVT* myNVT = NULL;
+  NPTi* myNPTi = NULL;
+  NPTf* myNPTf = NULL;
+  NPTxyz* myNPTxyz = NULL;
   
   for (k = 0; k < nInfo; k++){
     switch (ensembleCase){
-      case NVE_ENS:
-        if (globals->haveZconstraints()){
-          setupZConstraint(info[k]);
-          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
-        }
-        else{
-          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
-	}
+    case NVE_ENS:
+      if (globals->haveZconstraints()){
 	
+	std::cerr << "ZConstraint is temporarily disabled\n";
+	
+	// 	setupZConstraint(info[k]);
+	// 	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
+      }
+      
+//       else{
+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
+//       }
+	
 	info->the_integrator = myNVE;
         break;
+	
+    case NVT_ENS:
+      if (globals->haveZconstraints()){
 
-      case NVT_ENS:
-        if (globals->haveZconstraints()){
-          setupZConstraint(info[k]);
-          myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
-        }
+	std::cerr << "ZConstraint is temporarily disabled\n";
+
+// 	setupZConstraint(info[k]);
+// 	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
+      }
         else
           myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
 
@@ -1460,6 +1422,7 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauThermostat())
           myNPTf->setTauThermostat(globals->getTauThermostat());
+
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"
@@ -1470,6 +1433,7 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauBarostat())
           myNPTf->setTauBarostat(globals->getTauBarostat());
+
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"