--- trunk/mdtools/interface_implementation/SimSetup.cpp	2002/12/11 20:39:41	205
+++ trunk/mdtools/interface_implementation/SimSetup.cpp	2002/12/19 21:59:51	215
@@ -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",
@@ -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();
 
@@ -405,15 +407,21 @@ void SimSetup::createSim( void ){
 
 
 
-//   if( the_globals->haveInitialConfig() ){
-//        InitializeFromFile* fileInit;
-//     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
-
-//     fileInit->read_xyz( simnfo ); // default velocities on
+ 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{
+   delete fileInit;
+ }
+ else{
 
 #ifdef IS_MPI 
 
@@ -428,8 +436,10 @@ void SimSetup::createSim( void ){
 
   initFromBass();
 
-#endif // is_mpi
- 
+
+#endif
+ }
+
 #ifdef IS_MPI
   strcpy( checkPointMsg, "Successfully read in the initial configuration" );
   MPIcheckPoint();
@@ -439,7 +449,7 @@ void SimSetup::createSim( void ){
    
  
   
-  //   }
+
   
 #ifdef IS_MPI
   if( worldRank == 0 ){
@@ -575,8 +585,8 @@ 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;
@@ -642,14 +652,15 @@ void SimSetup::makeBonds( void ){
   the_bonds = new bond_pair[tot_bonds];
   index = 0;
   offset = 0;
-  molIndex = 0;
+  molIndex = 0;g1
+
   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 +703,8 @@ 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 +748,8 @@ 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++ ){