--- branches/development/src/brains/SimInfo.cpp	2010/12/31 18:31:56	1535
+++ branches/development/src/brains/SimInfo.cpp	2011/04/27 18:38:15	1549
@@ -55,6 +55,7 @@
 #include "primitives/Molecule.hpp"
 #include "primitives/StuntDouble.hpp"
 #include "UseTheForce/DarkSide/neighborLists_interface.h"
+#include "UseTheForce/doForces_interface.h"
 #include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
 #include "selection/SelectionManager.hpp"
@@ -131,7 +132,13 @@ namespace OpenMD {
     //equal to the total number of atoms minus number of atoms belong to 
     //cutoff group defined in meta-data file plus the number of cutoff 
     //groups defined in meta-data file
+    std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
+    std::cerr << "nCA = " << nCutoffAtoms << "\n";
+    std::cerr << "nG = " << nGroups << "\n";
+
     nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
+
+    std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
     
     //every free atom (atom does not belong to rigid bodies) is an 
     //integrable object therefore the total number of integrable objects 
@@ -776,8 +783,48 @@ namespace OpenMD {
     fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
     fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
     fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
+  }
+
+
+  vector<int> SimInfo::getGlobalAtomIndices() {
+    SimInfo::MoleculeIterator mi;
+    Molecule* mol;
+    Molecule::AtomIterator ai;
+    Atom* atom;
+
+    vector<int> GlobalAtomIndices(getNAtoms(), 0);
+    
+    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
+      
+      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
+	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
+      }
+    }
+    return GlobalAtomIndices;
+  }
+
+
+  vector<int> SimInfo::getGlobalGroupIndices() {
+    SimInfo::MoleculeIterator mi;
+    Molecule* mol;
+    Molecule::CutoffGroupIterator ci;
+    CutoffGroup* cg;
+
+    vector<int> GlobalGroupIndices;
+    
+    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
+      
+      //local index of cutoff group is trivial, it only depends on the
+      //order of travesing
+      for (cg = mol->beginCutoffGroup(ci); cg != NULL; 
+           cg = mol->nextCutoffGroup(ci)) {
+	GlobalGroupIndices.push_back(cg->getGlobalIndex());
+      }        
+    }
+    return GlobalGroupIndices;
   }
 
+
   void SimInfo::setupFortran() {
     int isError;
     int nExclude, nOneTwo, nOneThree, nOneFour;
@@ -817,16 +864,13 @@ namespace OpenMD {
       }       
     }
 
-    //fill ident array of local atoms (it is actually ident of
-    //AtomType, it is so confusing !!!)
-    vector<int> identArray;
+    // Build the identArray_
 
-    //to avoid memory reallocation, reserve enough space identArray
-    identArray.reserve(getNAtoms());
-    
+    identArray_.clear();
+    identArray_.reserve(getNAtoms());    
     for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
-	identArray.push_back(atom->getIdent());
+	identArray_.push_back(atom->getIdent());
       }
     }    
 
@@ -849,7 +893,7 @@ namespace OpenMD {
     int* oneThreeList = oneThreeInteractions_.getPairList();
     int* oneFourList = oneFourInteractions_.getPairList();
 
-    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], 
+    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], 
                    &nExclude, excludeList, 
                    &nOneTwo, oneTwoList,
                    &nOneThree, oneThreeList,
@@ -879,26 +923,8 @@ namespace OpenMD {
     }
    
 #ifdef IS_MPI    
-    //SimInfo is responsible for creating localToGlobalAtomIndex and
-    //localToGlobalGroupIndex
-    vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
-    vector<int> localToGlobalCutoffGroupIndex;
     mpiSimData parallelData;
 
-    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
-
-      //local index(index in DataStorge) of atom is important
-      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
-	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
-      }
-
-      //local index of cutoff group is trivial, it only depends on the order of travesing
-      for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
-	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
-      }        
-        
-    }
-
     //fill up mpiSimData struct
     parallelData.nMolGlobal = getNGlobalMolecules();
     parallelData.nMolLocal = getNMolecules();
@@ -910,9 +936,9 @@ namespace OpenMD {
     MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
 
     //pass mpiSimData struct and index arrays to fortran
-    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
-                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
-                    &localToGlobalCutoffGroupIndex[0], &isError);
+    //setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
+    //                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
+    //                &localToGlobalCutoffGroupIndex[0], &isError);
 
     if (isError) {
       sprintf(painCave.errMsg,
@@ -924,6 +950,14 @@ namespace OpenMD {
     sprintf(checkPointMsg, " mpiRefresh successful.\n");
     errorCheckPoint();
 #endif
+
+    initFortranFF(&isError);
+    if (isError) {
+      sprintf(painCave.errMsg,
+	      "initFortranFF errror: fortran didn't like something we gave it.\n");
+      painCave.isFatal = 1;
+      simError();
+    }
     fortranInitialized_ = true;
   }
 
@@ -961,9 +995,11 @@ namespace OpenMD {
     Molecule* mol;
     RigidBody* rb;
     Atom* atom;
+    CutoffGroup* cg;
     SimInfo::MoleculeIterator mi;
     Molecule::RigidBodyIterator rbIter;
-    Molecule::AtomIterator atomIter;;
+    Molecule::AtomIterator atomIter;
+    Molecule::CutoffGroupIterator cgIter;
  
     for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
         
@@ -974,6 +1010,10 @@ namespace OpenMD {
       for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
 	rb->setSnapshotManager(sman_);
       }
+
+      for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
+	cg->setSnapshotManager(sman_);
+      }
     }    
     
   }