--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/10/29 17:55:28	841
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/11/10 21:50:36	859
@@ -103,6 +103,10 @@ void SimSetup::createSim(void){
 
   sysObjectsCreation();
 
+  // check on the post processing info
+
+  finalInfoCheck();
+
   // initialize the system coordinates
 
   if ( !initSuspend ){
@@ -112,10 +116,6 @@ void SimSetup::createSim(void){
       info[0].currentTime = 0.0;
   }  
 
-  // check on the post processing info
-
-  finalInfoCheck();
-
   // make the output filenames
 
   makeOutNames();
@@ -699,6 +699,11 @@ void SimSetup::gatherInfo(void){
     
     if (globals->haveTempSet())
       info[i].setTemp = globals->getTempSet();
+
+    // check for the extended State init
+
+    info[i].useInitXSstate = globals->getUseInitXSstate();
+    info[i].orthoTolerance = globals->getOrthoBoxTolerance();
     
   }
   
@@ -776,18 +781,11 @@ void SimSetup::finalInfoCheck(void){
 
       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");
+                "SimSetup Warning: using default value of 15.0 angstroms"
+                "box length for the electrostaticCutoffRadius.\n");
         painCave.isFatal = 0;
         simError();
-        double smallest;
-        smallest = info[i].boxL[0];
-        if (info[i].boxL[1] <= smallest)
-          smallest = info[i].boxL[1];
-        if (info[i].boxL[2] <= smallest)
-          smallest = info[i].boxL[2];
-        theEcr = 0.5 * smallest;
+        theEcr = 15.0;
       }
       else{
         theEcr = globals->getECR();
@@ -820,23 +818,16 @@ 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[i].boxL[0];
-          if (info[i].boxL[1] <= smallest)
-            smallest = info[i].boxL[1];
-          if (info[i].boxL[2] <= smallest)
-            smallest = info[i].boxL[2];
-          theEcr = 0.5 * smallest;
+		  "SimSetup Warning: using default value of 15.0 angstroms"
+		  "box length for the electrostaticCutoffRadius.\n");
+	  painCave.isFatal = 0;
+	  simError();
+	  theEcr = 15.0;
         }
         else{
           theEcr = globals->getECR();
         }
-
+	
         if (!globals->haveEST()){
           sprintf(painCave.errMsg,
                   "SimSetup Warning: using default value of 0.05 * the "
@@ -849,18 +840,17 @@ void SimSetup::finalInfoCheck(void){
         else{
           theEst = globals->getEST();
         }
-
+	
         info[i].setDefaultEcr(theEcr, theEst);
       }
     }
   }
-
 #ifdef IS_MPI
   strcpy(checkPointMsg, "post processing checks out");
   MPIcheckPoint();
 #endif // is_mpi
 }
-
+  
 void SimSetup::initSystemCoords(void){
   int i;
 
@@ -888,21 +878,14 @@ void SimSetup::initSystemCoords(void){
     delete fileInit;
   }
   else{
-#ifdef IS_MPI 
-
+    
     // no init from bass
-
+    
     sprintf(painCave.errMsg,
-            "Cannot intialize a parallel simulation without an initial configuration file.\n");
+            "Cannot intialize a simulation without an initial configuration file.\n");
     painCave.isFatal = 1;;
     simError();
-
-#else
-
-    initFromBass();
-
-
-#endif
+    
   }
 
 #ifdef IS_MPI
@@ -1414,6 +1397,7 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauThermostat())
           myNPTf->setTauThermostat(globals->getTauThermostat());
+
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"
@@ -1424,6 +1408,7 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauBarostat())
           myNPTf->setTauBarostat(globals->getTauBarostat());
+
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"