--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/12/11 20:39:41	205
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2003/01/27 21:28:19	249
@@ -10,6 +10,7 @@
 
 #ifdef IS_MPI
 #include "mpiBASS.h"
+#include "mpiSimulation.hpp"
 #include "bassDiag.hpp"
 #endif
 
@@ -92,6 +93,7 @@ void SimSetup::createSim( void ){
   if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
   else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
   else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
+  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
   else{
     sprintf( painCave.errMsg,
 	     "SimSetup Error. Unrecognized force field -> %s\n",
@@ -187,7 +189,7 @@ void SimSetup::createSim( void ){
       if( currentStamp == NULL ){
 	sprintf( painCave.errMsg,
 		 "SimSetup error: Component \"%s\" was not found in the "
-		 "list of declared molecules\n"
+		 "list of declared molecules\n",
 		 id );
 	painCave.isFatal = 1;
 	simError();
@@ -234,7 +236,7 @@ void SimSetup::createSim( void ){
 
   // divide the molecules among processors here.
   
-  mpiSimulation* mpiSim = new mpiSimulation( simnfo );
+  mpiSim = new mpiSimulation( simnfo );
   
   mpiSim->divideLabor();
 
@@ -311,27 +313,8 @@ void SimSetup::createSim( void ){
   simnfo->sr_interactions = the_sris;
   simnfo->n_exclude = tot_SRI;
   simnfo->excludes = the_excludes;
-
-
-  // initialize the arrays
-
-  the_ff->setSimInfo( simnfo );
-
-  makeAtoms();
-
-  if( tot_bonds ){
-    makeBonds();
-  }
 
-  if( tot_bends ){
-    makeBends();
-  }
 
-  if( tot_torsions ){
-    makeTorsions();
-  }
-
-
   // get some of the tricky things that may still be in the globals
 
   if( simnfo->n_dipoles ){
@@ -404,17 +387,45 @@ void SimSetup::createSim( void ){
 #endif // is_mpi
 
 
-
-//   if( the_globals->haveInitialConfig() ){
-//        InitializeFromFile* fileInit;
-//     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
+  // initialize the arrays
 
-//     fileInit->read_xyz( simnfo ); // default velocities on
+  the_ff->setSimInfo( simnfo );
 
-//     delete fileInit;
-//   }
-//   else{
+  makeAtoms();
+
+  if( tot_bonds ){
+    makeBonds();
+  }
+
+  if( tot_bends ){
+    makeBends();
+  }
+
+  if( tot_torsions ){
+    makeTorsions();
+  }
+
+
+
+
+
+
+ if( the_globals->haveInitialConfig() ){
+ 
+     InitializeFromFile* fileInit;
+#ifdef IS_MPI // is_mpi
+     if( worldRank == 0 ){
+#endif //is_mpi
+   fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
+#ifdef IS_MPI
+     }else fileInit = new InitializeFromFile( NULL );
+#endif
+   fileInit->read_xyz( simnfo ); // default velocities on
 
+   delete fileInit;
+ }
+ else{
+
 #ifdef IS_MPI 
 
   // no init from bass
@@ -428,8 +439,10 @@ void SimSetup::createSim( void ){
 
   initFromBass();
 
-#endif // is_mpi
- 
+
+#endif
+ }
+
 #ifdef IS_MPI
   strcpy( checkPointMsg, "Successfully read in the initial configuration" );
   MPIcheckPoint();
@@ -439,7 +452,7 @@ void SimSetup::createSim( void ){
    
  
   
-  //   }
+
   
 #ifdef IS_MPI
   if( worldRank == 0 ){
@@ -550,13 +563,15 @@ void SimSetup::createSim( void ){
   if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
 
 
-  // make the longe range forces and the integrator
-
-  new AllLong( simnfo );
+//   // make the longe range forces and the integrator
 
-  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo );
+//   new AllLong( simnfo );
+
+  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
   if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo );
   if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo );
+  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
+
 }
 
 void SimSetup::makeAtoms( void ){
@@ -575,8 +590,8 @@ void SimSetup::makeAtoms( void ){
     for( j=0; j<components_nmol[i]; j++ ){
 
 #ifdef IS_MPI
-      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
-	  molIndex <= simnfo->mpiSim->getMyMolEnd() ){
+      if( mpiSim->getMyMolStart() <= molIndex &&
+	  molIndex <= mpiSim->getMyMolEnd() ){
 #endif // is_mpi	
 
 	molStart = index;
@@ -643,13 +658,14 @@ void SimSetup::makeBonds( void ){
   index = 0;
   offset = 0;
   molIndex = 0;
+
   for( i=0; i<n_components; i++ ){
 
     for( j=0; j<components_nmol[i]; j++ ){
 
 #ifdef IS_MPI
-      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
-	  molIndex <= simnfo->mpiSim->getMyMolEnd() ){
+      if( mpiSim->getMyMolStart() <= molIndex &&
+	  molIndex <= mpiSim->getMyMolEnd() ){
 #endif // is_mpi	
 	
 	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
@@ -692,8 +708,8 @@ void SimSetup::makeBends( void ){
     for( j=0; j<components_nmol[i]; j++ ){
 
 #ifdef IS_MPI
-      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
-	  molIndex <= simnfo->mpiSim->getMyMolEnd() ){
+      if( mpiSim->getMyMolStart() <= molIndex &&
+	  molIndex <= mpiSim->getMyMolEnd() ){
 #endif // is_mpi	
 
 	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
@@ -737,8 +753,8 @@ void SimSetup::makeTorsions( void ){
     for( j=0; j<components_nmol[i]; j++ ){
 
 #ifdef IS_MPI
-      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
-	  molIndex <= simnfo->mpiSim->getMyMolEnd() ){
+      if( mpiSim->getMyMolStart() <= molIndex &&
+	  molIndex <= mpiSim->getMyMolEnd() ){
 #endif // is_mpi	
 
       for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){