--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/10/17 21:59:12	144
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/11/21 20:33:06	184
@@ -6,6 +6,7 @@
 #include "parse_me.h"
 #include "LRI.hpp"
 #include "Integrator.hpp"
+#include "simError.h"
 
 #ifdef IS_MPI
 #include "mpiBASS.h"
@@ -15,6 +16,11 @@ SimSetup::SimSetup(){
 SimSetup::SimSetup(){
   stamps = new MakeStamps();
   globals = new Globals();
+  
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "SimSetup creation successful" );
+  MPIcheckPoint();
+#endif // IS_MPI
 }
 
 SimSetup::~SimSetup(){
@@ -24,14 +30,23 @@ void SimSetup::parseFile( char* fileName ){
 
 void SimSetup::parseFile( char* fileName ){
 
-  inFileName = fileName;
-  set_interface_stamps( stamps, globals );
 #ifdef IS_MPI
-  mpiEventInit();
+  if( worldRank == 0 ){
+#endif // is_mpi
+    
+    inFileName = fileName;
+    set_interface_stamps( stamps, globals );
+    
+#ifdef IS_MPI
+    mpiEventInit();
 #endif
-  yacc_BASS( fileName );
+
+    yacc_BASS( fileName );
+
 #ifdef IS_MPI
-  throwMPIEvent(NULL);
+    throwMPIEvent(NULL);
+  }
+  else receiveParse();
 #endif
 
 }
@@ -41,6 +56,7 @@ void SimSetup::receiveParse(void){
 
     set_interface_stamps( stamps, globals );
     mpiEventInit();
+    MPIcheckPoint();
     mpiEventLoop();
 
 }
@@ -52,6 +68,7 @@ void SimSetup::testMe(void){
   delete dumpMe;
 }
 #endif
+
 void SimSetup::createSim( void ){
 
   MakeStamps *the_stamps;
@@ -76,11 +93,18 @@ void SimSetup::createSim( void ){
   else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
   else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
   else{
-    std::cerr<< "SimSetup Error. Unrecognized force field -> "
-	     << force_field << "\n";
-    exit(8);
+    sprintf( painCave.errMsg,
+	     "SimSetup Error. Unrecognized force field -> %s\n",
+	     force_field );
+    painCave.isFatal = 1;
+    simError();
   }
 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "ForceField creation successful" );
+  MPIcheckPoint();
+#endif // is_mpi
+
   // get the components and calculate the tot_nMol and indvidual n_mol
   the_components = the_globals->getComponents();
   components_nmol = new int[n_components];
@@ -155,6 +179,7 @@ void SimSetup::createSim( void ){
 
   // create the atom and short range interaction arrays
 
+  Atom::createArrays(tot_atoms);
   the_atoms = new Atom*[tot_atoms];
   the_molecules = new Molecule[tot_nmol];
 
@@ -255,85 +280,98 @@ void SimSetup::createSim( void ){
 //   else{
 
     initFromBass();
-
-
-//   }
-
-//   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{
-//       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" );
-//       }
-//     }
-//   }
 
-//   // 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, ".mdl" ) ){
-//       strcpy( endTest, ".dump" );
-//     }
-//     else{
-//       strcat( simnfo->sampleName, ".dump" );
-//     }
-//   }
-
-//   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, ".mdl" ) ){
-//       strcpy( endTest, ".stat" );
-//     }
-//     else{
-//       strcat( simnfo->statusName, ".stat" );
-//     }
 //   }
 
+#ifdef IS_MPI
+    if( worldRank == TESTWRITE ){
+#endif // is_mpi
+      
+      fprintf( stderr, 
+	       "infile name is \"%s\"\n",
+	       inFileName );
+      
+      inFileName = "./butane.bass";
+	
+      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{
+	  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" );
+	  }
+	}
+      }
+      
+      // 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, ".mdl" ) ){
+	  strcpy( endTest, ".dump" );
+	}
+	else{
+	  strcat( simnfo->sampleName, ".dump" );
+	}
+      }
+      
+      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, ".mdl" ) ){
+	  strcpy( endTest, ".stat" );
+	}
+	else{
+	  strcat( simnfo->statusName, ".stat" );
+	}
+      }
+      
+#ifdef IS_MPI
+    }
+#endif // is_mpi
 
   // set the status, sample, and themal kick times
 
@@ -392,7 +430,7 @@ void SimSetup::makeAtoms( void ){
 	current_atom = comp_stamps[i]->getAtom( k );
 	if( current_atom->haveOrientation() ){
 
-	  dAtom = new DirectionalAtom;
+	  dAtom = new DirectionalAtom(index);
 	  simnfo->n_oriented++;
 	  the_atoms[index] = dAtom;
 
@@ -412,7 +450,7 @@ void SimSetup::makeAtoms( void ){
 	  dAtom->setSUz( uz );
 	}
 	else{
-	  the_atoms[index] = new GeneralAtom;
+	  the_atoms[index] = new GeneralAtom(index);
 	}
 	the_atoms[index]->setType( current_atom->getType() );
 	the_atoms[index]->setIndex( index );