--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/09/30 20:35:42	124
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/12/06 21:20:42	198
@@ -6,11 +6,21 @@
 #include "parse_me.h"
 #include "LRI.hpp"
 #include "Integrator.hpp"
-#include "mpiInterface.h"
+#include "simError.h"
 
+#ifdef IS_MPI
+#include "mpiBASS.h"
+#include "bassDiag.hpp"
+#endif
+
 SimSetup::SimSetup(){
   stamps = new MakeStamps();
   globals = new Globals();
+  
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "SimSetup creation successful" );
+  MPIcheckPoint();
+#endif // IS_MPI
 }
 
 SimSetup::~SimSetup(){
@@ -20,26 +30,43 @@ void SimSetup::parseFile( char* fileName ){
 
 void SimSetup::parseFile( char* fileName ){
 
-  inFileName = fileName;
-  set_interface_stamps( stamps, globals );
-#ifdef MPI
-  mpiEventInit();
+#ifdef IS_MPI
+  if( worldRank == 0 ){
+#endif // is_mpi
+    
+    inFileName = fileName;
+    set_interface_stamps( stamps, globals );
+    
+#ifdef IS_MPI
+    mpiEventInit();
 #endif
-  yacc_BASS( fileName );
-#ifdef MPI
-  throwMPIEvent(NULL);
+
+    yacc_BASS( fileName );
+
+#ifdef IS_MPI
+    throwMPIEvent(NULL);
+  }
+  else receiveParse();
 #endif
 
 }
 
-#ifdef MPI
+#ifdef IS_MPI
 void SimSetup::receiveParse(void){
 
     set_interface_stamps( stamps, globals );
     mpiEventInit();
+    MPIcheckPoint();
     mpiEventLoop();
 
 }
+
+
+void SimSetup::testMe(void){
+  bassDiag* dumpMe = new bassDiag(globals,stamps);
+  dumpMe->dumpStamps();
+  delete dumpMe;
+}
 #endif
 
 void SimSetup::createSim( void ){
@@ -66,11 +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];
@@ -85,9 +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();
@@ -95,32 +131,81 @@ 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.
+  // also extract the used stamps out into a separate linked list
 
+  simnfo->nComponents = n_components;
+  simnfo->componentsNmol = components_nmol;
+  simnfo->compStamps = comp_stamps;
+  simnfo->headStamp = new LinkedMolStamp();
+  
+  char* id;
+  LinkedMolStamp* headStamp = simnfo->headStamp;
+  LinkedMolStamp* currentStamp = NULL;
   for( i=0; i<n_components; i++ ){
 
-    comp_stamps[i] =
-      the_stamps->getMolecule( the_components[i]->getType() );
+    id = the_components[i]->getType();
+    comp_stamps[i] = NULL;
+    
+    // check to make sure the component isn't already in the list
+
+    comp_stamps[i] = headStamp->match( id );
+    if( comp_stamps[i] == NULL ){
+      
+      // extract the component from the list;
+      
+      currentStamp = the_stamps->extractMolStamp( id );
+      if( currentStamp == NULL ){
+	sprintf( painCave.errMsg,
+		 "SimSetup error: Component \"%s\" was not found in the "
+		 "list of declared molecules\n"
+		 id );
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      headStamp->add( currentStamp );
+      comp_stamps[i] = headStamp->match( id );
+    }
   }
 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
+  MPIcheckPoint();
+#endif // is_mpi
+  
 
 
+
   // caclulate the number of atoms, bonds, bends and torsions
 
   tot_atoms = 0;
@@ -142,16 +227,30 @@ void SimSetup::createSim( void ){
   simnfo->n_bends = tot_bends;
   simnfo->n_torsions = tot_torsions;
   simnfo->n_SRI = tot_SRI;
+  simnfo->n_mol = tot_nmol;
 
+  
+#ifdef IS_MPI
+
+  // divide the molecules among processors here.
+  
+  new mpiSimulation( simnfo );
+  
+  simnfo->mpiSim->divideLabor( n_components, comp_stamps, components_nmol );
+
+#endif // is_mpi
+  
+
   // create the atom and short range interaction arrays
 
-  the_atoms = new Atom*[tot_atoms];
-  the_molecules = new Molecule[tot_nmol];
+  Atom::createArrays(simnfo->n_atoms);
+  the_atoms = new Atom*[simnfo->n_atoms];
+  the_molecules = new Molecule[simnfo->n_mol];
 
 
-  if( tot_SRI ){
-    the_sris = new SRI*[tot_SRI];
-    the_excludes = new ex_pair[tot_SRI];
+  if( simnfo->n_SRI ){
+    the_sris = new SRI*[simnfo->n_SRI];
+    the_excludes = new ex_pair[simnfo->n_SRI];
   }
 
   // set the arrays into the SimInfo object
@@ -180,26 +279,34 @@ void SimSetup::createSim( void ){
     makeTorsions();
   }
 
-  //  makeMolecules();
 
   // get some of the tricky things that may still be in the globals
 
   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();
@@ -215,25 +322,37 @@ 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() );
@@ -244,89 +363,117 @@ void SimSetup::createSim( void ){
 //   }
 //   else{
 
-    initFromBass();
+#ifdef IS_MPI 
 
+  // no init from bass
+  
+  sprintf( painCave.errMsg,
+	   "Cannot intialize a parallel simulation without an initial configuration file.\n" );
+  painCave.isFatal;
+  simError();
+  
+#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" );
-//       }
-//     }
-//   }
+#endif // is_mpi
+ 
+#ifdef IS_MPI
+  strcpy( checkPointMsg, "Successfully read in the initial configuration" );
+  MPIcheckPoint();
+#endif // is_mpi
 
-//   // 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 == 0 ){
+#endif // is_mpi
+    
+    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
-
+  
   if( the_globals->haveSampleTime() ){
     simnfo->sampleTime = the_globals->getSampleTime();
     simnfo->statusTime = simnfo->sampleTime;
@@ -382,7 +529,7 @@ 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;
 
@@ -402,7 +549,7 @@ 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 );
@@ -549,8 +696,11 @@ 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{
@@ -655,12 +805,15 @@ 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() );