--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/10/22 21:17:32	812
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/11/06 22:01:37	855
@@ -1,10 +1,9 @@
 #include <algorithm>
-#include <cstdlib>
+#include <stdlib.h>
 #include <iostream>
-#include <cmath>
+#include <math.h>
 #include <string>
 #include <sprng.h> 
-
 #include "SimSetup.hpp"
 #include "ReadWrite.hpp"
 #include "parse_me.h"
@@ -32,6 +31,8 @@ SimSetup::SimSetup(){
 using namespace std;
 
 SimSetup::SimSetup(){
+  
+  initSuspend = false;
   isInfoArray = 0;
   nInfo = 1;
 
@@ -54,6 +55,7 @@ void SimSetup::setSimInfo(SimInfo* the_info, int theNi
   info = the_info;
   nInfo = theNinfo;
   isInfoArray = 1;
+  initSuspend = true;
 }
 
 
@@ -100,20 +102,20 @@ void SimSetup::createSim(void){
   // creation of complex system objects
 
   sysObjectsCreation();
-
-  // check on the post processing info
-
-  finalInfoCheck();
 
   // initialize the system coordinates
 
-  if (!isInfoArray){
+  if ( !initSuspend ){
     initSystemCoords();
 
     if( !(globals->getUseInitTime()) )
       info[0].currentTime = 0.0;
   }  
 
+  // check on the post processing info
+
+  finalInfoCheck();
+
   // make the output filenames
 
   makeOutNames();
@@ -694,58 +696,17 @@ 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
+    // check for the extended State init
 
-    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);
-    }
+    info[i].useInitXSstate = globals->getUseInitXSstate();
+    info[i].orthoTolerance = globals->getOrthoBoxTolerance();
+    
   }
-
+  
   //setup seed for random number generator
   int seedValue;
 
@@ -849,7 +810,7 @@ void SimSetup::finalInfoCheck(void){
         theEst = globals->getEST();
       }
 
-      info[i].setEcr(theEcr, theEst);
+      info[i].setDefaultEcr(theEcr, theEst);
 
       if (!globals->haveDielectric()){
         sprintf(painCave.errMsg,
@@ -894,9 +855,12 @@ void SimSetup::finalInfoCheck(void){
           theEst = globals->getEST();
         }
 
-        info[i].setEcr(theEcr, theEst);
+        info[i].setDefaultEcr(theEcr, theEst);
       }
     }
+
+    if( !initSuspend )
+      info[i].checkCutOffs();
   }
 
 #ifdef IS_MPI
@@ -1458,6 +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"
@@ -1468,6 +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"