--- trunk/OOPSE/libmdtools/SimSetup.hpp	2003/03/26 20:22:02	407
+++ trunk/OOPSE/libmdtools/SimSetup.hpp	2004/06/01 18:42:58	1214
@@ -6,9 +6,10 @@
 #include "ForceFields.hpp"
 #include "SimInfo.hpp"
 #include "ReadWrite.hpp"
+#include "AllIntegrator.hpp"
 
 // this routine is defined in BASS_interface.cpp
-void set_interface_stamps( MakeStamps* ms, Globals* g );
+extern void set_interface_stamps( MakeStamps* ms, Globals* g );
 
 class SimSetup{
 
@@ -16,7 +17,9 @@ class SimSetup{ (public)
   SimSetup();
   ~SimSetup();
 
-  void setSimInfo( SimInfo* the_simnfo ) { simnfo = the_simnfo; }
+  void setSimInfo( SimInfo* the_info ) { info = the_info; }
+  void setSimInfo( SimInfo* the_info, int theNinfo );
+  void suspendInit( void ) { initSuspend = true; }  
   void parseFile( char* fileName );
   void createSim( void );
 
@@ -27,23 +30,48 @@ class SimSetup{ (public)
   void receiveParse(void);
 #endif
 
-  void makeMolecules( void );
+  void gatherInfo( void );
+  void sysObjectsCreation( void );
+  void finalInfoCheck( void );
+  void initSystemCoords( void );
+  void makeOutNames(void);
+  void makeIntegrator(void);
+  void initFortran(void);
+  void makeMinimizer(void);
 
-  void makeAtoms( void );
-  void makeBonds( void );
-  void makeBends( void );
-  void makeTorsions( void );
+  void createFF( void );
+  void compList( void );
+  void calcSysValues( void );
+  void makeSysArrays( void );
 
+#ifdef IS_MPI
+  void mpiMolDivide( void );
+
+  int* mol2proc;
+  int* molCompType;
+
+#endif //is_mpi
+
   void initFromBass( void );
+  void makeMolecules( void );
   void makeElement( double x, double y, double z );
 
+  int ensembleCase;
+  int ffCase;
+
   MakeStamps* stamps;
   Globals* globals;
   char* inFileName;
 
-  SimInfo* simnfo;
+  SimInfo* info;
+  int isInfoArray;
+  int nInfo;
+  
+  bool initSuspend;
 
   int n_components;
+  int globalAtomCounter;
+  int globalMolCounter;
 
   char force_field[100];
   char ensemble[100];
@@ -53,15 +81,13 @@ class SimSetup{ (public)
   MoleculeStamp** comp_stamps; //the stamps matching the components
   int tot_nmol;
   int tot_atoms;
+  int tot_groups;
+  int tot_rigid;
   int tot_bonds;
   int tot_bends;
   int tot_torsions;
   int tot_SRI;
 
-  Atom** the_atoms;
-  SRI** the_sris;
-  int *the_excludes;
-  Molecule* the_molecules;
   ForceFields* the_ff;
 
   // needed by makeElement
@@ -71,9 +97,9 @@ class SimSetup{ (public)
   int current_comp;
   int current_atom_ndx;
 
-#ifdef IS_MPI
-  int* globalIndex;
-#endif //is_mpi
+  vector<int> globalAtomIndex;
+  vector<int> globalGroupIndex;
+  void setupZConstraint(SimInfo& theInfo);  //setup parameters for zconstraint method
 
 };
 #endif