--- branches/development/src/brains/SimInfo.hpp	2010/12/31 18:31:56	1535
+++ branches/development/src/brains/SimInfo.hpp	2011/05/26 13:55:04	1569
@@ -63,14 +63,10 @@
 #include "utils/PropertyMap.hpp"
 #include "utils/LocalIndexManager.hpp"
 #include "nonbonded/SwitchingFunction.hpp"
-
-//another nonsense macro declaration
-#define __OPENMD_C
-#include "brains/fSimulation.h"
 
 using namespace std;
 namespace OpenMD{
-  //forward decalration 
+  //forward declaration 
   class SnapshotManager;
   class Molecule;
   class SelectionManager;
@@ -302,9 +298,9 @@ namespace OpenMD{
 
     void update();
     /**
-     * Setup Fortran Simulation
+     * Do final bookkeeping before Force managers need their data.
      */
-    void setupFortran();
+    void prepareTopology();
 
 
     /** Returns the local index manager */
@@ -341,6 +337,21 @@ namespace OpenMD{
     int getGlobalMolMembership(int id){
       return globalMolMembership_[id];
     }
+
+    /** 
+     * returns a vector which maps the local atom index on this
+     * processor to the global atom index.  With only one processor,
+     * these should be identical.
+     */
+    vector<int> getGlobalAtomIndices();
+
+    /** 
+     * returns a vector which maps the local cutoff group index on
+     * this processor to the global cutoff group index.  With only one
+     * processor, these should be identical.
+     */
+    vector<int> getGlobalGroupIndices();
+
         
     string getFinalConfigFileName() {
       return finalConfigFileName_;
@@ -400,8 +411,8 @@ namespace OpenMD{
     }
 
 
-    bool isFortranInitialized() {
-      return fortranInitialized_;
+    bool isTopologyDone() {
+      return topologyDone_;
     }
         
     bool getCalcBoxDipole() {
@@ -532,15 +543,14 @@ namespace OpenMD{
     bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
     bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
     bool usesMetallicAtoms() { return usesMetallicAtoms_; }
+    bool usesAtomicVirial() { return usesAtomicVirial_; }
+    bool requiresPrepair() { return requiresPrepair_; }
+    bool requiresSkipCorrection() { return requiresSkipCorrection_;}
+    bool requiresSelfCorrection() { return requiresSelfCorrection_;}
 
   private:
     /// Data structures holding primary simulation objects
     map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
-    simtype fInfo_;                   /**< A dual struct shared by C++
-                                         and Fortran to pass
-                                         information about what types
-                                         of calculation are
-                                         required */
 
     /// Stamps are templates for objects that are then used to create
     /// groups of objects.  For example, a molecule stamp contains
@@ -557,6 +567,9 @@ namespace OpenMD{
      * the simulation.  It should be nGlobalAtoms_ in size.
      */
     vector<int> globalGroupMembership_; 
+  public:
+    vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
+  private:
 
     /**
      * A vector that maps between the global index of an atom and the
@@ -564,7 +577,29 @@ namespace OpenMD{
      * by SimCreator once and only once, since it is never changed
      * during the simulation. It shoudl be nGlobalAtoms_ in size.
      */
-    vector<int> globalMolMembership_;        
+    vector<int> globalMolMembership_; 
+
+    /** 
+     * A vector that maps between the local index of an atom and the
+     * index of the AtomType.
+     */
+    vector<int> identArray_;
+  public:
+    vector<int> getIdentArray() { return identArray_; }
+  private:
+    
+    /** 
+     * A vector which contains the fractional contribution of an
+     * atom's mass to the total mass of the cutoffGroup that atom
+     * belongs to.  In the case of single atom cutoff groups, the mass
+     * factor for that atom is 1.  For massless atoms, the factor is
+     * also 1.
+     */
+    vector<RealType> massFactors_;
+  public:
+    vector<RealType> getMassFactors() { return massFactors_; }
+  private:
+
                
     /// lists to handle atoms needing special treatment in the non-bonded interactions
     PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
@@ -595,7 +630,9 @@ namespace OpenMD{
     string restFileName_;
         
 
-    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
+    bool topologyDone_;  /** flag to indicate whether the topology has
+                             been scanned and all the relevant
+                             bookkeeping has been done*/
     
     bool calcBoxDipole_; /**< flag to indicate whether or not we calculate 
                             the simulation box dipole moment */