--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/10/29 17:55:28	841
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/01/19 18:36:21	962
@@ -30,6 +30,30 @@ using namespace std;
 
 using namespace std;
 
+/**
+ * Check whether dividend is divisble by divisor or not
+ */
+bool isDivisible(double dividend, double divisor){
+  double tolerance = 0.000001;
+  double quotient;
+  double diff;
+  int intQuotient;
+  
+  quotient = dividend / divisor;
+
+  if (quotient < 0)
+    quotient = -quotient;
+
+  intQuotient = int (quotient + tolerance);
+
+  diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
+
+  if (diff <= tolerance)
+    return true;
+  else
+    return false;  
+}
+
 SimSetup::SimSetup(){
   
   initSuspend = false;
@@ -103,6 +127,10 @@ void SimSetup::createSim(void){
 
   sysObjectsCreation();
 
+  // check on the post processing info
+
+  finalInfoCheck();
+
   // initialize the system coordinates
 
   if ( !initSuspend ){
@@ -111,10 +139,6 @@ void SimSetup::createSim(void){
     if( !(globals->getUseInitTime()) )
       info[0].currentTime = 0.0;
   }  
-
-  // check on the post processing info
-
-  finalInfoCheck();
 
   // make the output filenames
 
@@ -665,8 +689,37 @@ void SimSetup::gatherInfo(void){
             " Please give nMol in the components.\n");
     painCave.isFatal = 1;
     simError();
+  }
+
+  //check whether sample time, status time, thermal time and reset time are divisble by dt
+  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
+    sprintf(painCave.errMsg,
+              "Sample time is not divisible by dt \n");
+    painCave.isFatal = 0;
+    simError();    
+  }
+
+  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
+    sprintf(painCave.errMsg,
+              "Status time is not divisible by dt\n");
+    painCave.isFatal = 0;
+    simError();    
   }
 
+  if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
+    sprintf(painCave.errMsg,
+              "Thermal time is not divisible by dt\n");
+    painCave.isFatal = 0;
+    simError();    
+  }  
+
+  if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
+    sprintf(painCave.errMsg,
+              "Reset time is not divisible by dt\n");
+    painCave.isFatal = 0;
+    simError();    
+  } 
+
   // set the status, sample, and thermal kick times
 
   for (i = 0; i < nInfo; i++){
@@ -699,6 +752,11 @@ 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 +834,11 @@ 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 +871,16 @@ 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 +893,17 @@ 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 +931,14 @@ 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 +1450,7 @@ 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 +1461,7 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauBarostat())
           myNPTf->setTauBarostat(globals->getTauBarostat());
+
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"