--- trunk/OOPSE/libmdtools/SimSetup.hpp	2003/08/12 17:51:33	682
+++ trunk/OOPSE/libmdtools/SimSetup.hpp	2004/06/01 18:42:58	1214
@@ -19,6 +19,7 @@ class SimSetup{ (public)
 
   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 );
 
@@ -36,6 +37,7 @@ class SimSetup{ (public)
   void makeOutNames(void);
   void makeIntegrator(void);
   void initFortran(void);
+  void makeMinimizer(void);
 
   void createFF( void );
   void compList( void );
@@ -57,7 +59,6 @@ class SimSetup{ (public)
   int ensembleCase;
   int ffCase;
 
-
   MakeStamps* stamps;
   Globals* globals;
   char* inFileName;
@@ -65,9 +66,12 @@ class SimSetup{ (public)
   SimInfo* info;
   int isInfoArray;
   int nInfo;
+  
+  bool initSuspend;
 
   int n_components;
-  int globalAtomIndex;
+  int globalAtomCounter;
+  int globalMolCounter;
 
   char force_field[100];
   char ensemble[100];
@@ -77,6 +81,8 @@ 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;
@@ -91,10 +97,8 @@ 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
 
 };