--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/11/21 20:33:06	184
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/11/26 21:04:43	189
@@ -119,9 +119,11 @@ void SimSetup::createSim( void ){
 
       if( !the_components[i]->haveNMol() ){
 	// we have a problem
-	std::cerr << "SimSetup Error. No global NMol or component NMol"
-		  << " given. Cannot calculate the number of atoms.\n";
-	exit( 8 );
+	sprintf( painCave.errMsg,
+		 "SimSetup Error. No global NMol or component NMol"
+		 " given. Cannot calculate the number of atoms.\n" );
+	painCave.isFatal = 1;
+	simError();
       }
 
       tot_nmol += the_components[i]->getNMol();
@@ -129,22 +131,35 @@ void SimSetup::createSim( void ){
     }
   }
   else{
-    std::cerr << "NOT A SUPPORTED FEATURE\n";
-
-//     tot_nmol = the_globals->getNMol();
-
-//     //we have the total number of molecules, now we check for molfractions
-//     for( i=0; i<n_components; i++ ){
-
-//       if( !the_components[i]->haveMolFraction() ){
-
-// 	if( !the_components[i]->haveNMol() ){
-// 	  //we have a problem
-// 	  std::cerr << "SimSetup error. Neither molFraction nor "
-// 		    << " nMol was given in component
-
+    sprintf( painCave.errMsg,
+	     "SimSetup error.\n"
+	     "\tSorry, the ability to specify total"
+	     " nMols and then give molfractions in the components\n"
+	     "\tis not currently supported."
+	     " Please give nMol in the components.\n" );
+    painCave.isFatal = 1;
+    simError();
+    
+    
+    //     tot_nmol = the_globals->getNMol();
+    
+    //   //we have the total number of molecules, now we check for molfractions
+    //     for( i=0; i<n_components; i++ ){
+    
+    //       if( !the_components[i]->haveMolFraction() ){
+    
+    // 	if( !the_components[i]->haveNMol() ){
+    // 	  //we have a problem
+    // 	  std::cerr << "SimSetup error. Neither molFraction nor "
+    // 		    << " nMol was given in component
+    
   }
 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Have the number of components" );
+  MPIcheckPoint();
+#endif // is_mpi
+
   // make an array of molecule stamps that match the components used.
 
   for( i=0; i<n_components; i++ ){
@@ -222,19 +237,28 @@ void SimSetup::createSim( void ){
   if( simnfo->n_dipoles ){
 
     if( !the_globals->haveRRF() ){
-      std::cerr << "SimSetup Error, system has dipoles, but no rRF was set.\n";
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "SimSetup Error, system has dipoles, but no rRF was set.\n");
+      painCave.isFatal = 1;
+      simError();
     }
     if( !the_globals->haveDielectric() ){
-      std::cerr << "SimSetup Error, system has dipoles, but no"
-		<< " dielectric was set.\n";
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "SimSetup Error, system has dipoles, but no"
+	       " dielectric was set.\n" );
+      painCave.isFatal = 1;
+      simError();
     }
 
     simnfo->rRF        = the_globals->getRRF();
     simnfo->dielectric = the_globals->getDielectric();
   }
 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "rRf and dielectric check out" );
+  MPIcheckPoint();
+#endif // is_mpi
+  
   if( the_globals->haveBox() ){
     simnfo->box_x = the_globals->getBox();
     simnfo->box_y = the_globals->getBox();
@@ -250,25 +274,37 @@ void SimSetup::createSim( void ){
   }
   else{
     if( !the_globals->haveBoxX() ){
-      std::cerr << "SimSetup error, no periodic BoxX size given.\n";
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "SimSetup error, no periodic BoxX size given.\n" );
+      painCave.isFatal = 1;
+      simError();
     }
     simnfo->box_x = the_globals->getBoxX();
 
     if( !the_globals->haveBoxY() ){
-      std::cerr << "SimSetup error, no periodic BoxY size given.\n";
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "SimSetup error, no periodic BoxY size given.\n" );
+      painCave.isFatal = 1;
+      simError();
     }
     simnfo->box_y = the_globals->getBoxY();
 
     if( !the_globals->haveBoxZ() ){
-      std::cerr << "SimSetup error, no periodic BoxZ size given.\n";
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "SimSetup error, no periodic BoxZ size given.\n" );
+      painCave.isFatal = 1;
+      simError();
     }
     simnfo->box_z = the_globals->getBoxZ();
   }
 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Box size set up" );
+  MPIcheckPoint();
+#endif // is_mpi
 
+
+
 //   if( the_globals->haveInitialConfig() ){
 //        InitializeFromFile* fileInit;
 //     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
@@ -279,102 +315,104 @@ void SimSetup::createSim( void ){
 //   }
 //   else{
 
-    initFromBass();
+  initFromBass();
+ 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "initFromBass successfully created the lattice" );
+  MPIcheckPoint();
+#endif // is_mpi
 
 
-//   }
-
+   
+ 
+  
+  //   }
+  
 #ifdef IS_MPI
-    if( worldRank == TESTWRITE ){
+  if( worldRank == 0 ){
 #endif // is_mpi
-      
-      fprintf( stderr, 
-	       "infile name is \"%s\"\n",
-	       inFileName );
-      
-      inFileName = "./butane.bass";
-	
-      if( the_globals->haveFinalConfig() ){
-	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
+    
+    if( the_globals->haveFinalConfig() ){
+      strcpy( simnfo->finalName, the_globals->getFinalConfig() );
+    }
+    else{
+      strcpy( simnfo->finalName, inFileName );
+      char* endTest;
+      int nameLength = strlen( simnfo->finalName );
+      endTest = &(simnfo->finalName[nameLength - 5]);
+      if( !strcmp( endTest, ".bass" ) ){
+	strcpy( endTest, ".eor" );
+      }
+      else if( !strcmp( endTest, ".BASS" ) ){
+	strcpy( endTest, ".eor" );
       }
       else{
-	strcpy( simnfo->finalName, inFileName );
-	char* endTest;
-	int nameLength = strlen( simnfo->finalName );
-	endTest = &(simnfo->finalName[nameLength - 5]);
-	if( !strcmp( endTest, ".bass" ) ){
+	endTest = &(simnfo->finalName[nameLength - 4]);
+	if( !strcmp( endTest, ".bss" ) ){
 	  strcpy( endTest, ".eor" );
 	}
-	else if( !strcmp( endTest, ".BASS" ) ){
+	else if( !strcmp( endTest, ".mdl" ) ){
 	  strcpy( endTest, ".eor" );
 	}
 	else{
-	  endTest = &(simnfo->finalName[nameLength - 4]);
-	  if( !strcmp( endTest, ".bss" ) ){
-	    strcpy( endTest, ".eor" );
-	  }
-	  else if( !strcmp( endTest, ".mdl" ) ){
-	    strcpy( endTest, ".eor" );
-	  }
-	  else{
-	    strcat( simnfo->finalName, ".eor" );
-	  }
+	  strcat( simnfo->finalName, ".eor" );
 	}
       }
-      
-      // make the sample and status out names
-      
-      strcpy( simnfo->sampleName, inFileName );
-      char* endTest;
-      int nameLength = strlen( simnfo->sampleName );
-      endTest = &(simnfo->sampleName[nameLength - 5]);
-      if( !strcmp( endTest, ".bass" ) ){
+    }
+    
+    // make the sample and status out names
+    
+    strcpy( simnfo->sampleName, inFileName );
+    char* endTest;
+    int nameLength = strlen( simnfo->sampleName );
+    endTest = &(simnfo->sampleName[nameLength - 5]);
+    if( !strcmp( endTest, ".bass" ) ){
+      strcpy( endTest, ".dump" );
+    }
+    else if( !strcmp( endTest, ".BASS" ) ){
+      strcpy( endTest, ".dump" );
+    }
+    else{
+      endTest = &(simnfo->sampleName[nameLength - 4]);
+      if( !strcmp( endTest, ".bss" ) ){
 	strcpy( endTest, ".dump" );
       }
-      else if( !strcmp( endTest, ".BASS" ) ){
+      else if( !strcmp( endTest, ".mdl" ) ){
 	strcpy( endTest, ".dump" );
       }
       else{
-	endTest = &(simnfo->sampleName[nameLength - 4]);
-	if( !strcmp( endTest, ".bss" ) ){
-	  strcpy( endTest, ".dump" );
-	}
-	else if( !strcmp( endTest, ".mdl" ) ){
-	  strcpy( endTest, ".dump" );
-	}
-	else{
-	  strcat( simnfo->sampleName, ".dump" );
-	}
+	strcat( simnfo->sampleName, ".dump" );
       }
-      
-      strcpy( simnfo->statusName, inFileName );
-      nameLength = strlen( simnfo->statusName );
-      endTest = &(simnfo->statusName[nameLength - 5]);
-      if( !strcmp( endTest, ".bass" ) ){
+    }
+    
+    strcpy( simnfo->statusName, inFileName );
+    nameLength = strlen( simnfo->statusName );
+    endTest = &(simnfo->statusName[nameLength - 5]);
+    if( !strcmp( endTest, ".bass" ) ){
+      strcpy( endTest, ".stat" );
+    }
+    else if( !strcmp( endTest, ".BASS" ) ){
+      strcpy( endTest, ".stat" );
+    }
+    else{
+      endTest = &(simnfo->statusName[nameLength - 4]);
+      if( !strcmp( endTest, ".bss" ) ){
 	strcpy( endTest, ".stat" );
       }
-      else if( !strcmp( endTest, ".BASS" ) ){
+      else if( !strcmp( endTest, ".mdl" ) ){
 	strcpy( endTest, ".stat" );
       }
       else{
-	endTest = &(simnfo->statusName[nameLength - 4]);
-	if( !strcmp( endTest, ".bss" ) ){
-	  strcpy( endTest, ".stat" );
-	}
-	else if( !strcmp( endTest, ".mdl" ) ){
-	  strcpy( endTest, ".stat" );
-	}
-	else{
-	  strcat( simnfo->statusName, ".stat" );
-	}
+	strcat( simnfo->statusName, ".stat" );
       }
-      
-#ifdef IS_MPI
     }
-#endif // is_mpi
-
+    
+#ifdef IS_MPI
+  }
+#endif // is_mpi
+  
   // set the status, sample, and themal kick times
-
+  
   if( the_globals->haveSampleTime() ){
     simnfo->sampleTime = the_globals->getSampleTime();
     simnfo->statusTime = simnfo->sampleTime;
@@ -597,8 +635,11 @@ void SimSetup::initFromBass( void ){
     n_per_extra = (int)ceil( temp1 );
 
     if( n_per_extra > 4){
-      std::cerr << "THere has been an error in constructing the non-complete lattice.\n";
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "SimSetup error. There has been an error in constructing"
+	       " the non-complete lattice.\n" );
+      painCave.isFatal = 1;
+      simError();
     }
   }
   else{
@@ -703,12 +744,15 @@ void SimSetup::makeElement( double x, double y, double
 
     current_atom = comp_stamps[current_comp]->getAtom( k );
     if( !current_atom->havePosition() ){
-      std::cerr << "Component " << comp_stamps[current_comp]->getID()
-		<< ", atom " << current_atom->getType()
-		<< " does not have a position specified.\n"
-		<< "The initialization routine is unable to give a start"
-		<< " position.\n";
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "SimSetup:initFromBass error.\n"
+	       "\tComponent %s, atom %s does not have a position specified.\n"
+	       "\tThe initialization routine is unable to give a start"
+	       " position.\n",
+	       comp_stamps[current_comp]->getID(),
+	       current_atom->getType() );
+      painCave.isFatal = 1;
+      simError();
     }
 
     the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );