--- trunk/OOPSE/libmdtools/SimSetup.hpp	2003/10/27 22:07:48	823
+++ trunk/OOPSE/libmdtools/SimSetup.hpp	2004/06/01 18:42:58	1214
@@ -37,6 +37,7 @@ class SimSetup{ (private)
   void makeOutNames(void);
   void makeIntegrator(void);
   void initFortran(void);
+  void makeMinimizer(void);
 
   void createFF( void );
   void compList( void );
@@ -58,7 +59,6 @@ class SimSetup{ (private)
   int ensembleCase;
   int ffCase;
 
-
   MakeStamps* stamps;
   Globals* globals;
   char* inFileName;
@@ -70,7 +70,8 @@ class SimSetup{ (private)
   bool initSuspend;
 
   int n_components;
-  int globalAtomIndex;
+  int globalAtomCounter;
+  int globalMolCounter;
 
   char force_field[100];
   char ensemble[100];
@@ -80,6 +81,8 @@ class SimSetup{ (private)
   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;
@@ -94,10 +97,8 @@ class SimSetup{ (private)
   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
 
 };