// Copyright (c) Lawrence Livermore National Security, LLC and other VisIt
// Project developers.  See the top-level LICENSE file for dates and other
// details.  No copyright assignment is required to contribute to VisIt.

// ************************************************************************* //
//                            avtFLASHFileFormat.C                           //
// ************************************************************************* //

#include <avtFLASHFileFormat.h>

#include <string>
#include <vector>
#include <algorithm>

#include <vtkFloatArray.h>
#include <vtkRectilinearGrid.h>
#include <vtkUnstructuredGrid.h>
#include <vtkCellType.h>
#include <vtkPolyData.h>
#include <vtkCellArray.h>

#include <vtkPointData.h>
#include <vtkVisItUtility.h>

#include <float.h>
#include <algorithm>

#include <avtDatabase.h>
#include <avtDatabaseMetaData.h>
#include <avtVariableCache.h>
#include <avtStructuredDomainBoundaries.h>
#include <avtStructuredDomainNesting.h>
#include <avtIntervalTree.h>

#include <DBOptionsAttributes.h>

#include <Expression.h>

#include <InvalidVariableException.h>
#include <InvalidFilesException.h>
#include <DebugStream.h>
#include <TimingsManager.h>

// Define this symbol BEFORE including hdf5.h to indicate the HDF5 code
// in this file uses version 1.6 of the HDF5 API. This is harmless for
// versions of HDF5 before 1.8 and ensures correct compilation with
// version 1.8 and thereafter. When, and if, the HDF5 code in this file
// is explicitly upgraded to the 1.8 API, this symbol should be removed.
#define H5_USE_16_API
#include <vtk_hdf5.h>
#include <visit-hdf5.h>


//  "file format version" == 8.  Uses NDIM (value 1, 2 or 3) for size of 2nd 
//  index of "bounding box", "coordinates" & "block size"
#define FLASH3_FFV8 8

//  "file format version" == 9.  Uses MDIM (value always 3) for size of 2nd 
//  index of "bounding box", "coordinates" & "block size"
#define FLASH3_FFV9 9

//  Until further notice, this (maximum dimension) will always be "3"
#define MDIM 3


using std::find;
using std::string;
using std::vector;

int avtFLASHFileFormat::objcnt = 0;

// ****************************************************************************
//  Function:  GetNiceParticleName
//
//  Purpose:
//    Nicely group particle names into a subdirectory.
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 25, 2005
//
// ****************************************************************************
static string GetNiceParticleName(const string &varname)
{
    string nicename = varname;
    if (nicename.length() > 9 && nicename.substr(0,9) == "particle_")
    {
        nicename = string("Particles/") + nicename.substr(9);
    }
    else
    {
        nicename = string("Particles/") + nicename;
    }
    return nicename;
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::Block::Print
//
//  Programmer:  Jeremy Meredith
//  Creation:    September 27, 2005
//
//  Changes:
//    Randy Hudson, June 12, 2007
//    Added printing of node type, block-center coordinates and processor number.
//
// ****************************************************************************
void
avtFLASHFileFormat::Block::Print(ostream &out)
{
    out << "---- BLOCK: "<<ID<<endl;
    out << "  level = "<<level<<endl;
    out << "  node type = "<<nodetype<<endl;
    out << "  coordinates of block center = ";
    for (int c=0; c<3; c++)
        out << coords[c]<< " ";
    out << endl;
    out << "  processor number = "<<procnum<<endl;
    out << "  parentID = "<<parentID<<endl;
    out << "  childrenIDs = ";
    for (int c=0; c<8; c++)
        out << childrenIDs[c]<< " ";
    out << endl;
    out << "  neighborIDs = ";
    for (int n=0; n<6; n++)
        out << neighborIDs[n]<< " ";
    out << endl;
    out << "  minSpatialExtents = "
         << minSpatialExtents[0] << " , "
         << minSpatialExtents[1] << " , "
         << minSpatialExtents[2] << endl;
    out << "  maxSpatialExtents = "
         << maxSpatialExtents[0] << " , "
         << maxSpatialExtents[1] << " , "
         << maxSpatialExtents[2] << endl;
    out << "  minGlobalLogicalExtents = "
         << minGlobalLogicalExtents[0] << " , "
         << minGlobalLogicalExtents[1] << " , "
         << minGlobalLogicalExtents[2] << endl;
    out << "  maxGlobalLogicalExtents = "
         << maxGlobalLogicalExtents[0] << " , "
         << maxGlobalLogicalExtents[1] << " , "
         << maxGlobalLogicalExtents[2] << endl;
}

// ****************************************************************************
//  Function:  avtFLASHFileFormat::InitializeHDF5
//
//  Purpose:   Initialize interaction with the HDF5 library
//
//  Programmer:  Mark C. Miller
//  Creation:    Decmeber 10, 2003
//
// ****************************************************************************
void
avtFLASHFileFormat::InitializeHDF5(void)
{
    debug5 << "Initializing HDF5 Library" << endl;
    H5open();
    H5Eset_auto(NULL, NULL);
}

// ****************************************************************************
//  Function:  avtFLASHFileFormat::FinalizeHDF5
//
//  Purpose:   End interaction with the HDF5 library
//
//  Programmer:  Mark C. Miller
//  Creation:    March 5, 2007 
//
//  Modifications:
//
//    Mark C. Miller, Tue Apr 14 17:21:23 PDT 2009
//    Replaced call to H5close with H5garbage_collect. Calling H5close is 
//    problematic as VisIt may have other plugins instantiated which are
//    still interacting with HDF5. Calling garbage collect routine achieves
//    the desired goal of reducing memory usage without effecting other
//    plugins that might still be using the HDF5 library. 
// ****************************************************************************
void
avtFLASHFileFormat::FinalizeHDF5(void)
{
    debug5 << "Garbage collecting HDF5 Library" << endl;
    H5garbage_collect();
}

// ****************************************************************************
//  Method: avtFLASH constructor
//
//  Programmer: Jeremy Meredith
//  Creation:   August 23, 2005
//
//  Modifications:
//
//    Mark C. Miller, Mon Mar  5 22:04:50 PST 2007
//    Added initialization of HDF5, simParamsHaveBeenRead
//
//    Randy Hudson, July 5, 2007
//    Moved initialization of numProcessors here from ReadProcessorNumbers()
//
//    Randy Hudson, July 10, 2007
//    Added initialization of file_has_procnum
//
//    Randy Hudson, January 30, 2008
//    Added initialization of fileFormatVersion
//
//    Hank Childs, Thu Dec 17 14:07:52 PST 2009
//    Added database options (for toggling between processors or levels).
//
//    Hank Childs, Sat Mar 20 20:21:47 PDT 2010
//    Initialize new database options options.
//
// ****************************************************************************

avtFLASHFileFormat::avtFLASHFileFormat(const char *cfilename, 
                                       const DBOptionsAttributes *opts)
    : avtSTMDFileFormat(&cfilename, 1)
{
    filename  = cfilename;
    fileId    = -1;
    dimension = 0;
    numBlocks = 0;
    numLevels = 0;
    numProcessors = 0;
    file_has_procnum = false;
    fileFormatVersion = -1;

    showProcessors = opts->GetBool("Show generating processor instead of refinement level");
    newStyleCurves = opts->GetBool("Use new style curve generation");
    addStructuredDomainBoundaries = opts->GetBool("Set up patch abutment information");

    // do HDF5 library initialization on consturction of first instance
    if (avtFLASHFileFormat::objcnt == 0)
        InitializeHDF5();
    avtFLASHFileFormat::objcnt++;
}


// ****************************************************************************
//  Function:  avtFLASHFileFormat::~avtFLASHFileFormat
//
//  Purpose:   Destructor; free up resources, including hdf5 lib 
//
//  Programmer:  Mark C. Miller
//  Creation:    March 5, 2007 
//
// ****************************************************************************
avtFLASHFileFormat::~avtFLASHFileFormat()
{
    FreeUpResources();

    // handle HDF5 library termination on descrution of last instance
    avtFLASHFileFormat::objcnt--;
    if (avtFLASHFileFormat::objcnt == 0)
        FinalizeHDF5();
}

// ****************************************************************************
//  Method: avtFLASHFileFormat::ActivateTimestep
//
//  Purpose:
//      Tells the reader to activate the current time step.  This means 
//      rebuilding the nesting structure if it is not available.
//
//  Programmer: Hank Childs
//  Creation:   April 28, 2006
//
// ****************************************************************************

void
avtFLASHFileFormat::ActivateTimestep(void)
{
    BuildDomainNesting();
}

// ****************************************************************************
//  Method: avtFLASHFileFormat::GetCycle
//
//  Purpose: Do as little work on file meta data as possible to get
//  current cycle
//
//  Programmer: Mark C. Miller 
//  Creation:   March 5, 2007 
//
//  Modifications:
//    Mark C. Miller, Tue Mar  6 23:41:33 PST 2007
//    Removed optimization to avoid re-reading simulation parameters between
//    calls to GetCycle and/or GetTime because we actually need to do only
//    a partial read of them.
//
// ****************************************************************************

int
avtFLASHFileFormat::GetCycle()
{
    const bool timeAndCycleOnly = true;
    hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
    if (file_id < 0)
        return INVALID_CYCLE;
    ReadVersionInfo(file_id);
    ReadSimulationParameters(file_id, timeAndCycleOnly);
    H5Fclose(file_id);
    return simParams.nsteps;
}

// ****************************************************************************
//  Method: avtFLASHFileFormat::GetCycle
//
//  Purpose: Do as little work on file meta data as possible to get
//  current time 
//
//  Programmer: Mark C. Miller 
//  Creation:   March 5, 2007 
//
//  Modifications:
//    Mark C. Miller, Tue Mar  6 23:41:33 PST 2007
//    Removed optimization to avoid re-reading simulation parameters between
//    calls to GetCycle and/or GetTime because we actually need to do only
//    a partial read of them.
//
// ****************************************************************************

double
avtFLASHFileFormat::GetTime()
{
    const bool timeAndCycleOnly = true;
    hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
    if (file_id < 0)
        return INVALID_TIME;
    ReadVersionInfo(file_id);
    ReadSimulationParameters(file_id, timeAndCycleOnly);
    H5Fclose(file_id);
    return simParams.time;
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::FreeUpResources
//
//  Purpose:
//      When VisIt is done focusing on a particular timestep, it asks that
//      timestep to free up any resources (memory, file descriptors) that
//      it has associated with it.  This method is the mechanism for doing
//      that.
//
//  Programmer: Jeremy Meredith
//  Creation:   August 23, 2005
//
//  Modifications:
//    Jeremy Meredith, Thu Aug 25 15:07:36 PDT 2005
//    Added particle support.
//
//    Randy Hudson, June 23, 2007
//    Added code for vector of leaf blocks for morton curve.
//
// ****************************************************************************

void
avtFLASHFileFormat::FreeUpResources(void)
{
    if (fileId >= 0)
    {
        H5Fclose(fileId);
        fileId = -1;
    }
    blocks.clear();
    varNames.clear();
    particleVarNames.clear();
    particleVarTypes.clear();
    particleOriginalIndexMap.clear();
    leafBlocks.clear();
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::PopulateDatabaseMetaData
//
//  Purpose:
//      This database meta-data object is like a table of contents for the
//      file.  By populating it, you are telling the rest of VisIt what
//      information it can request from you.
//
//  Programmer: Jeremy Meredith
//  Creation:   August 23, 2005
//
//  Modifications:
//    Jeremy Meredith, Thu Aug 25 15:07:36 PDT 2005
//    Added particle support.
//
//    Jeremy Meredith, Tue Sep 27 14:23:17 PDT 2005
//    Added support for files containing only particles and no grids.
//
//    Jeremy Meredith, Thu Sep 29 11:12:29 PDT 2005
//    Added conversion of 1D grids to curves.
//
//    Hank Childs, Wed Jan 11 09:40:17 PST 2006
//    Change mesh type to AMR.
//
//    Randy Hudson, Apr 3, 2007
//    Added support for Morton curve.
//
//    Randy Hudson, June 12, 2007
//    Added support for subsets by processor number.
//
//    Randy Hudson, June 18, 2007
//    Added support for creating subsets of Morton curve.
//
//    Randy Hudson, July 19, 2007
//    Added support for concurrent block-level and block-processor subset pairs
//      for both domain and morton curve meshes
//
//    Hank Childs, Fri Dec 11 11:37:48 PST 2009
//    Add support for more efficient AMR data structure.
//
//    Hank Childs, Thu Dec 17 14:07:52 PST 2009
//    Added database options (for toggling between processors or levels).
//
// ****************************************************************************

void
avtFLASHFileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData *md)
{
    ReadAllMetaData();

    BuildDomainNesting();

    // grids
    //    for block and level SIL categories
    if (numBlocks > 0)
    {
        avtMeshMetaData *mesh = new avtMeshMetaData;
        mesh->name = "amr_mesh";
        mesh->originalName = "amr_mesh";

        mesh->meshType = AVT_AMR_MESH;
        mesh->topologicalDimension = dimension;
        mesh->spatialDimension = dimension;
        mesh->blockOrigin = 1;
        mesh->groupOrigin = 1;

        mesh->hasSpatialExtents = true;
        mesh->minSpatialExtents[0] = minSpatialExtents[0];
        mesh->maxSpatialExtents[0] = maxSpatialExtents[0];
        mesh->minSpatialExtents[1] = minSpatialExtents[1];
        mesh->maxSpatialExtents[1] = maxSpatialExtents[1];
        mesh->minSpatialExtents[2] = minSpatialExtents[2];
        mesh->maxSpatialExtents[2] = maxSpatialExtents[2];

        mesh->SetAMRInfo("level", "block", 1, patchesPerLevel);
        md->Add(mesh);

        // grid variables
        for (size_t v = 0 ; v < varNames.size(); v++)
        {
            // Create var names for unique submenu for block and level
            AddScalarVarToMetaData(md, varNames[v], "amr_mesh", AVT_ZONECENT);
        }

        avtMeshMetaData *mcblmesh = new avtMeshMetaData;
        mcblmesh->name = "morton_blockandlevel";
        mcblmesh->originalName = "morton_blockandlevel";

        mcblmesh->meshType = AVT_UNSTRUCTURED_MESH;
        mcblmesh->topologicalDimension = 1;    //    It's a curve
        mcblmesh->spatialDimension = dimension;
        mcblmesh->blockOrigin = 1;
        mcblmesh->groupOrigin = 1;

        mcblmesh->hasSpatialExtents = true;
        mcblmesh->minSpatialExtents[0] = minSpatialExtents[0];
        mcblmesh->maxSpatialExtents[0] = maxSpatialExtents[0];
        mcblmesh->minSpatialExtents[1] = minSpatialExtents[1];
        mcblmesh->maxSpatialExtents[1] = maxSpatialExtents[1];
        mcblmesh->minSpatialExtents[2] = minSpatialExtents[2];
        mcblmesh->maxSpatialExtents[2] = maxSpatialExtents[2];

        // DEFINING SUBSETS ON M. CURVE MESH (LIKE THAT ON BASE MESH "mesh")
        // spoof a group/domain mesh for the AMR hierarchy
        mcblmesh->numBlocks = numBlocks;
        mcblmesh->blockTitle = "Blocks";
        mcblmesh->blockPieceName = "block";
        // Level as group
        mcblmesh->numGroups = numLevels;
        mcblmesh->groupTitle = "Levels";
        mcblmesh->groupPieceName = "level";
        mcblmesh->numGroups = numLevels;

        mcblmesh->blockNameScheme = mesh->blockNameScheme;
        mcblmesh->groupIdsBasedOnRange = mesh->groupIdsBasedOnRange;

        md->Add(mcblmesh);
    }

    if (showProcessors)
    {
        //    for block and processor SIL categories
        if (numBlocks > 0)
        {
            avtMeshMetaData *bpmesh = new avtMeshMetaData;
            bpmesh->originalName = "mesh_blockandproc";
            bpmesh->name = "mesh_blockandproc";
    
            bpmesh->meshType = AVT_AMR_MESH;
            bpmesh->topologicalDimension = dimension;
            bpmesh->spatialDimension = dimension;
            bpmesh->blockOrigin = 1;
            bpmesh->groupOrigin = 0;
    
            bpmesh->hasSpatialExtents = true;
            bpmesh->minSpatialExtents[0] = minSpatialExtents[0];
            bpmesh->maxSpatialExtents[0] = maxSpatialExtents[0];
            bpmesh->minSpatialExtents[1] = minSpatialExtents[1];
            bpmesh->maxSpatialExtents[1] = maxSpatialExtents[1];
            bpmesh->minSpatialExtents[2] = minSpatialExtents[2];
            bpmesh->maxSpatialExtents[2] = maxSpatialExtents[2];
    
            // spoof a group/domain mesh for the AMR hierarchy
            bpmesh->numBlocks = numBlocks;
            bpmesh->blockTitle = "Blocks";
            bpmesh->blockPieceName = "block";
            // Processor number as group
            bpmesh->numGroups = numProcessors;
            bpmesh->groupTitle = "Processors";
            bpmesh->groupPieceName = "processor";
            bpmesh->numGroups = numProcessors;
    
            vector<int> groupIds(numBlocks);
            vector<string> pieceNames(numBlocks);
            // Processor number as group
            for (int i = 0; i < numBlocks; i++)
            {
                char tmpName[64];
                sprintf(tmpName,"processor%d,block%d",blocks[i].procnum, blocks[i].ID);
                groupIds[i] = blocks[i].procnum;
                pieceNames[i] = tmpName;
            }
            bpmesh->blockNames = pieceNames;
            bpmesh->groupIds = groupIds;
            md->Add(bpmesh);
    
            // grid variables
            for (size_t v = 0 ; v < varNames.size(); v++)
            {
                // Create var names for unique submenu for block and level
                string composite = "mesh_blockandproc/" + varNames[v];
                AddScalarVarToMetaData(md, composite, "mesh_blockandproc", AVT_ZONECENT);
            }
        }
    }

    // curves
    if (numBlocks > 0 && dimension == 1)
    {
        // grid variables
        for (size_t v = 0 ; v < varNames.size(); v++)
        {
            avtCurveMetaData *curve = new avtCurveMetaData;
            curve->name = string("curves/") + varNames[v];
            md->Add(curve);
        }
        
    }

    // particles
    if (numParticles > 0)
    {
        // particle mesh
        avtMeshMetaData *pmesh = new avtMeshMetaData;
        pmesh->name = "particles";
        pmesh->originalName = "particles";

        pmesh->meshType = AVT_POINT_MESH;
        pmesh->topologicalDimension = 0;
        pmesh->spatialDimension = dimension;
        pmesh->cellOrigin = 1;
        pmesh->hasSpatialExtents = false;
        pmesh->numBlocks = 1;
        pmesh->numGroups = 0;
        md->Add(pmesh);

        // particle variables
        for (size_t pv = 0 ; pv < particleVarNames.size(); pv++)
        {
            AddScalarVarToMetaData(md,
                                   GetNiceParticleName(particleVarNames[pv]),
                                   "particles", AVT_NODECENT);
        }

    }

    if (showProcessors)
    {
        //    for block and processor SIL categories
        if (numBlocks > 0)
        {
            avtMeshMetaData *mcbpmesh = new avtMeshMetaData;
            mcbpmesh->name = "morton_blockandproc";
            mcbpmesh->originalName = "morton_blockandproc";
    
            mcbpmesh->meshType = AVT_UNSTRUCTURED_MESH;
            mcbpmesh->topologicalDimension = 1;    //    It's a curve
            mcbpmesh->spatialDimension = dimension;
            mcbpmesh->blockOrigin = 1;
            mcbpmesh->groupOrigin = 0;
    
            mcbpmesh->hasSpatialExtents = true;
            mcbpmesh->minSpatialExtents[0] = minSpatialExtents[0];
            mcbpmesh->maxSpatialExtents[0] = maxSpatialExtents[0];
            mcbpmesh->minSpatialExtents[1] = minSpatialExtents[1];
            mcbpmesh->maxSpatialExtents[1] = maxSpatialExtents[1];
            mcbpmesh->minSpatialExtents[2] = minSpatialExtents[2];
            mcbpmesh->maxSpatialExtents[2] = maxSpatialExtents[2];
    
            // DEFINING SUBSETS ON M. CURVE MESH (LIKE THAT ON BASE MESH "mesh")
            // spoof a group/domain mesh for the AMR hierarchy
            mcbpmesh->numBlocks = numBlocks;
            mcbpmesh->blockTitle = "Blocks";
            mcbpmesh->blockPieceName = "block";
            // Processor number as group
            mcbpmesh->numGroups = numProcessors;
            mcbpmesh->groupTitle = "Processors";
            mcbpmesh->groupPieceName = "processor";
            mcbpmesh->numGroups = numProcessors;
    
            vector<int> groupIds(numBlocks);
            vector<string> pieceNames(numBlocks);
            // Processor number as group
            for (int i = 0; i < numBlocks; i++)
            {
                char tmpName[64];
                sprintf(tmpName,"processor%d,block%d",blocks[i].procnum, blocks[i].ID);
                groupIds[i] = blocks[i].procnum;
                pieceNames[i] = tmpName;
            }
            mcbpmesh->blockNames = pieceNames;
            mcbpmesh->groupIds = groupIds;

            md->Add(mcbpmesh);
        }
    }

    // Populate cycle and time
    md->SetCycle(timestep, simParams.nsteps);
    md->SetTime(timestep, simParams.time);
    md->SetCycleIsAccurate(true, timestep);
    md->SetTimeIsAccurate(true, timestep);
}


// ****************************************************************************
//  Function: QsortCurveSorter
//
//  Purpose:
//      Sorts the left-hand-side location for a curve, keeping the block ID
//      along with the sort.
//
//  Programmer: Hank Childs
//  Creation:   March 19, 2010
//
// ****************************************************************************


typedef struct
{
    double f;
    int   b;
} DoubleInt;


static int
QsortCurveSorter(const void *arg1, const void *arg2)
{
    DoubleInt *A = (DoubleInt *) arg1;
    DoubleInt *B = (DoubleInt *) arg2;

    if (A->f < B->f)
        return -1;
    else if (B->f < A->f)
        return 1;

    // equal start.  Return the coarser blocks first.  (Coarser blocks have 
    // lower block numbers)
    if (A->b < B->b)
        return -1;
    if (B->b < A->b)
        return 1;

    return 0;
}

// ****************************************************************************
//  Method: avtFLASHFileFormat::GetMesh
//
//  Purpose:
//      Gets the mesh associated with this file.  The mesh is returned as a
//      derived type of vtkDataSet (ie vtkRectilinearGrid, vtkStructuredGrid,
//      vtkUnstructuredGrid, etc).
//
//  Arguments:
//      domain      The index of the domain.  If there are NDomains, this
//                  value is guaranteed to be between 0 and NDomains-1,
//                  regardless of block origin.
//      meshname    The name of the mesh of interest.  This can be ignored if
//                  there is only one mesh.
//
//  Programmer: Jeremy Meredith
//  Creation:   August 23, 2005
//
//  Modifications:
//    Jeremy Meredith, Thu Aug 25 15:07:36 PDT 2005
//    Added particle support.
//
//    Jeremy Meredith, Tue Sep 27 14:23:42 PDT 2005
//    Added "new" style particle support where the HDF5 variable name
//    containing particle data has changed.
//
//    Jeremy Meredith, Thu Sep 29 11:12:50 PDT 2005
//    Added support for converting 1D AMR grids to curves.
//
//    Kathleen Bonnell, Thu Jul 20 11:22:13 PDT 2006
//    Added support for FLASH3 formats.
//
//    Randy Hudson, Apr 3, 2007
//    Added support for Morton curve.
//
//    Randy Hudson, June 18, 2007
//    Added support for creating subsets of Morton curve.
//
//    Randy Hudson, July 19, 2007
//    Added support for concurrent block-level and block-processor subset pairs
//      for both domain and morton curve meshes
//
//    Randy Hudson, June 10, 2008
//    Replaced the representation of curves as vtkPolyData with that as 
//      vtkRectilinearGrid, to support expressions
//
//    Brad Whitlock, Wed Nov 18 11:10:09 PST 2009
//    Delete double precision particle data.
//
//    Hank Childs, Fri Dec 11 13:15:13 PST 2009
//    Add support for reordering of indices for SIL efficiencies.
//
//    Hank Childs, Fri Mar 19 11:06:49 PDT 2010
//    Do not flatten curves ... leave them as AMR.
//
//    Gunther H. Weber, Mon Jul 28 18:15:48 PDT 2014
//    Add meta data requried by AMRStitchCell operator.
//
// ****************************************************************************

vtkDataSet *
avtFLASHFileFormat::GetMesh(int domain, const char *meshname)
{
    ReadAllMetaData();

    if (string(meshname) == "amr_mesh")
    {
        int theRealDomain = visitIdToFLASHId[domain];
        // rectilinear mesh
        vtkFloatArray  *coords[3];
        int i;
        for (i = 0 ; i < 3 ; i++)
        {
            coords[i] = vtkFloatArray::New();
            coords[i]->SetNumberOfTuples(block_ndims[i]);
            for (int j = 0 ; j < block_ndims[i] ; j++)
            {
                if (i+1 > dimension)
                {
                    coords[i]->SetComponent(j, 0, 0);
                }
                else
                {
                    double minExt = blocks[theRealDomain].minSpatialExtents[i];
                    double maxExt = blocks[theRealDomain].maxSpatialExtents[i];
                    double c = minExt + double(j) *
                        (maxExt-minExt) / double(block_ndims[i]-1);
                    coords[i]->SetComponent(j, 0, c);
                }
            }
        }
   
        vtkRectilinearGrid  *rGrid = vtkRectilinearGrid::New(); 
        rGrid->SetDimensions(block_ndims);
        rGrid->SetXCoordinates(coords[0]);
        coords[0]->Delete();
        rGrid->SetYCoordinates(coords[1]);
        coords[1]->Delete();
        rGrid->SetZCoordinates(coords[2]);
        coords[2]->Delete();

        vtkIntArray *arr = vtkIntArray::New();
        arr->SetNumberOfTuples(3);
        arr->SetValue(0, blocks[theRealDomain].minGlobalLogicalExtents[0]);
        arr->SetValue(1, blocks[theRealDomain].minGlobalLogicalExtents[1]);
        arr->SetValue(2, blocks[theRealDomain].minGlobalLogicalExtents[2]);
        arr->SetName("base_index");
        rGrid->GetFieldData()->AddArray(arr);
        arr->Delete();

        return rGrid;
    }
    else if (string(meshname) == "mesh_blockandproc")
    {
        // rectilinear mesh
        vtkFloatArray  *coords[3];
        int i;
        for (i = 0 ; i < 3 ; i++)
        {
            coords[i] = vtkFloatArray::New();
            coords[i]->SetNumberOfTuples(block_ndims[i]);
            for (int j = 0 ; j < block_ndims[i] ; j++)
            {
                if (i+1 > dimension)
                {
                    coords[i]->SetComponent(j, 0, 0);
                }
                else
                {
                    double minExt = blocks[domain].minSpatialExtents[i];
                    double maxExt = blocks[domain].maxSpatialExtents[i];
                    double c = minExt + double(j) *
                        (maxExt-minExt) / double(block_ndims[i]-1);
                    coords[i]->SetComponent(j, 0, c);
                }
            }
        }
   
        vtkRectilinearGrid  *rGrid = vtkRectilinearGrid::New(); 
        rGrid->SetDimensions(block_ndims);
        rGrid->SetXCoordinates(coords[0]);
        coords[0]->Delete();
        rGrid->SetYCoordinates(coords[1]);
        coords[1]->Delete();
        rGrid->SetZCoordinates(coords[2]);
        coords[2]->Delete();

        return rGrid;
    }
    else if (string(meshname) == "particles")
    {
        hid_t pointId = H5Dopen(fileId, particleHDFVarName.c_str());

        vtkPoints *points  = vtkPoints::New();
        points->SetNumberOfPoints(numParticles);
        float *pts = (float *) points->GetVoidPointer(0);
        int i/*, index = 0*/;

        hid_t xtype = 0, ytype = 0, ztype = 0;  //TODO: check on fix for uninitialized pointer
 
        double *ddata = new double[numParticles];
        if (fileFormatVersion < FLASH3_FFV8)
        {
            xtype = H5Tcreate(H5T_COMPOUND, sizeof(double));
            ytype = H5Tcreate(H5T_COMPOUND, sizeof(double));
            ztype = H5Tcreate(H5T_COMPOUND, sizeof(double));
            H5Tinsert(xtype, "particle_x", 0, H5T_NATIVE_DOUBLE);
            H5Tinsert(ytype, "particle_y", 0, H5T_NATIVE_DOUBLE);
            H5Tinsert(ztype, "particle_z", 0, H5T_NATIVE_DOUBLE);
        }
        if (dimension >= 1)
        {
            if (fileFormatVersion < FLASH3_FFV8)
            {
                H5Dread(pointId, xtype, H5S_ALL,H5S_ALL,H5P_DEFAULT, ddata);
            }
            else 
            {
                ReadParticleVar(pointId, "Particles/posx", ddata);
            }
            for (i=0; i<numParticles; i++)
            {
                pts[i*3+0] = float(ddata[i]);
            }
 
        }

        if (dimension >= 2)
        {
            if (fileFormatVersion < FLASH3_FFV8) 
            {
                H5Dread(pointId, ytype, H5S_ALL,H5S_ALL,H5P_DEFAULT, ddata);
            }
            else 
            {
                ReadParticleVar(pointId, "Particles/posy", ddata);
            }
            for (i=0; i<numParticles; i++)
            {
                pts[i*3+1] = float(ddata[i]);
            }
        }

        if (dimension >= 3)
        {
            if (fileFormatVersion < FLASH3_FFV8) 
            {
                 H5Dread(pointId, ztype, H5S_ALL,H5S_ALL,H5P_DEFAULT, ddata);
            }
            else 
            {
                ReadParticleVar(pointId, "Particles/posz", ddata);
            }
            for (i=0; i<numParticles; i++)
            {
                pts[i*3+2] = float(ddata[i]);
            }
        }
        delete [] ddata;

        // fill in zeros
        for (int d=dimension; d<3; d++)
        {
            for (i=0; i<numParticles; i++)
                pts[i*3 + d] = 0;
        }

        if (fileFormatVersion < FLASH3_FFV8)
        {
            H5Tclose(xtype);
            H5Tclose(ytype);
            H5Tclose(ztype);
        }
        H5Dclose(pointId);

        vtkUnstructuredGrid  *ugrid = vtkUnstructuredGrid::New(); 
        ugrid->SetPoints(points);
        ugrid->Allocate(numParticles);
        vtkIdType onevertex;
        for(i = 0; i < numParticles; ++i)
        {
            onevertex = i;
            ugrid->InsertNextCell(VTK_VERTEX, 1, &onevertex);
        }

        points->Delete();

        return ugrid;
    }
    else if (strlen(meshname) > 7 && strncmp(meshname, "curves/", 7)==0)
    {
        int b,i;

        //
        // Read the values from the file
        //
        int nvals = block_zdims[0] * numBlocks;
        float *vals = new float[nvals];

        string varname = string(meshname).substr(7); 
        hid_t varId = H5Dopen(fileId, varname.c_str());

        H5Dread(varId, H5T_NATIVE_FLOAT, H5S_ALL,H5S_ALL,H5P_DEFAULT, vals);
        H5Dclose(varId);

        if (newStyleCurves)
        {
            if (numBlocks <= 0)
            {
                delete [] vals;
                return NULL;
            }
    
            //
            // Get info about each segment.
            //
            DoubleInt *di = new DoubleInt[numBlocks];
            for (b=0; b<numBlocks; b++)
            {
                 di[b].f = blocks[b].minSpatialExtents[0];
                 di[b].b = b;
            }
    
            vector<double> xvals;
            vector<double> yvals;

            // Sort them from left to right.
            qsort(di, numBlocks, sizeof(DoubleInt), QsortCurveSorter);
    
            vector<int> blocksInProgress;
            blocksInProgress.push_back(di[0].b);
            double curLocation = blocks[di[0].b].minSpatialExtents[0];
            int    lastBlockIdx = 1;
            int    blocksInProgressIdx = 0;
            while (blocksInProgressIdx >= 0)
            {
                int curBlock  = blocksInProgress[blocksInProgressIdx];
                int nextBlock = di[lastBlockIdx].b;
                double goUntilLocation;
                if (lastBlockIdx >= numBlocks)
                {
                     // we are at the last block.
                    goUntilLocation = blocks[curBlock].maxSpatialExtents[0];
                }
                else
                    goUntilLocation = blocks[nextBlock].minSpatialExtents[0];
    
                bool curBlockWillEnd = false;
                if (goUntilLocation >= blocks[curBlock].maxSpatialExtents[0])
                {
                    curBlockWillEnd = true;
                    goUntilLocation = blocks[curBlock].maxSpatialExtents[0];
                }
    
                // We know that we want to add points for "curBlock" from "curLocation"
                // to "goUntilLocation".
                if (curLocation < goUntilLocation)
                {
                    double minExt = blocks[curBlock].minSpatialExtents[0];
                    double maxExt = blocks[curBlock].maxSpatialExtents[0];
                    double step = (maxExt-minExt) / block_zdims[0];
                    int start = (int) floor((curLocation-minExt)/step);
                    int stop  = (int) ceil((goUntilLocation-minExt)/step);
                    if (start < 0)
                        start = 0;
                    if (stop >= block_zdims[0])
                        stop = block_zdims[0]-1;
                    for (int j = start ; j <= stop ; j++)
                    {
                        double x = minExt + j*step + step/2.;
                        if (x < curLocation || x > goUntilLocation)
                            continue;
                        xvals.push_back(x);
                        yvals.push_back(vals[curBlock*block_zdims[0] + j]);
                    }
                }
                curLocation = goUntilLocation;
    
                if (curBlockWillEnd)
                {
                    // continue with the previous block.  If the new block
                    // starts, we will figure that out on the next iteration.
                    // This statement corresponds to a no-op.  However,
                    // if we have no blocks queued up, then the logic would end.
                    // So test for that.
                    if (lastBlockIdx < numBlocks && blocksInProgressIdx <= 0)
                    {
                        blocksInProgress[0] = nextBlock;
                        blocksInProgressIdx = 0;
                        lastBlockIdx++;
                    }
                    else
                        blocksInProgressIdx--;
                }
                else
                {
                    // queue up the old block and put the new block in.
                    blocksInProgressIdx++;
                    blocksInProgress.resize(blocksInProgressIdx+1);
                    blocksInProgress[blocksInProgressIdx] = nextBlock;
                    lastBlockIdx++;
                }
            }

            //
            // Add all of the points to an array.
            //
            int nPts = xvals.size();
            vtkRectilinearGrid *rg = vtkVisItUtility::Create1DRGrid(nPts,VTK_FLOAT);
            vtkFloatArray    *valarray = vtkFloatArray::New();
            valarray->SetNumberOfComponents(1);
            valarray->SetNumberOfTuples(nPts);
            valarray->SetName(meshname);
            rg->GetPointData()->SetScalars(valarray);
            vtkDataArray *xc = rg->GetXCoordinates();
            for (int j = 0 ; j < nPts ; j++)
            {
                //  NODE CENTERED:
                xc->SetComponent(j,  0, xvals[j]);
                
                valarray->SetValue(j, yvals[j]);
            }
            valarray->Delete();    
    
            delete[] vals;
        
            return rg;
        }
        else
        {    
            //
            // Find a sampling
            //
            double ds_size   = maxSpatialExtents[0] - minSpatialExtents[0];
            double step_size = ds_size;

            for (b=0; b<numBlocks; b++)
            {
                double minExt = blocks[b].minSpatialExtents[0];
                double maxExt = blocks[b].maxSpatialExtents[0];
                double step   = (maxExt - minExt) / double(block_zdims[0]);
                if (step < step_size)
                    step_size = step;
            }
            int nsteps = int(.5 + (ds_size / step_size));
   
            //
            // Create and initialize the sampling arrays
            //
            float *x = new float[nsteps];
            float *y = new float[nsteps];
            float *l = new float[nsteps];
  
            for (i=0; i<nsteps; i++)
            {
                x[i] = (step_size * (double(i)+.5)) + minSpatialExtents[0];
                y[i] = 0;
                l[i] = -1;
            }
    
            //
            // Sample each block
            //
            for (b=0; b<numBlocks; b++)
            {
                double minExt = blocks[b].minSpatialExtents[0];
                double maxExt = blocks[b].maxSpatialExtents[0];
                double size   = maxExt - minExt;
                double step   = size / double(block_zdims[0]);
    
                int first_index = int((minExt - (minSpatialExtents[0]+step_size/2.))/step_size+.99999);
                int last_index  = int((maxExt - (minSpatialExtents[0]+step_size/2.))/step_size);
    
                if (first_index < 0 || first_index >= nsteps)
                {
                    // Logic error!  Recover.
                    first_index = 0;
                }
                if (last_index < 0 || last_index >= nsteps)
                {
                    // Logic error!  Recover.
                    last_index = nsteps-1;
                }
    
                for (int j = first_index; j <= last_index; j++)
                {
                    if (blocks[b].level < l[j])
                        continue;
    
                    int block_index = int((x[j] - minExt) / step);
                    if (block_index < 0 || block_index >= block_zdims[0])
                    {
                        // Logic error! Could be propagated from earlier. Recover.
                        continue;
                    }

                    y[j] = vals[b * block_zdims[0] + block_index];
                    l[j] = blocks[b].level;
                }
            }
    
            //
            // Create the rectilinear grid
            //   (Lifted from avtCurve2DFileFormat::ReadFile())
            //
    
            //
            // Add all of the points to an array.
            //
            int nPts = nsteps;
            vtkRectilinearGrid *rg = vtkVisItUtility::Create1DRGrid(nPts,VTK_FLOAT);
            vtkFloatArray    *valarray = vtkFloatArray::New();
            valarray->SetNumberOfComponents(1);
            valarray->SetNumberOfTuples(nPts);
            valarray->SetName(meshname);
            rg->GetPointData()->SetScalars(valarray);
            vtkDataArray *xc = rg->GetXCoordinates();
            for (int j = 0 ; j < nPts ; j++)
            {
                //  NODE CENTERED:
                xc->SetComponent(j,  0, x[j]);
                
                valarray->SetValue(j, y[j]);
            }
            valarray->Delete();    
    
            delete[] vals;
            delete[] x;
            delete[] y;
            delete[] l;
        
            return rg;
        }
    }
    else if (string(meshname) == "morton_blockandlevel")
    {
        return GetMortonCurveSubset(domain);
    }
    else if (string(meshname) == "morton_blockandproc")
    {
        return GetMortonCurveSubset(domain);
    }

    return NULL;
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::GetMortonCurveSubset
//          (Version of GetMortonCurve() for subsets)
//
//  Purpose:
//      Build and return the subset, for block "domain", of the Morton space-filling
//         curve as a vtkPolyData object.
//      The morton curve connects leaf blocks.
//      The two segments of the curve that enter and leave block "domain" are built.
//
//  Programmer: Randy Hudson
//  Creation:   June 15, 2007
//
//  Modifications:
//    Brad Whitlock, Wed Nov 18 11:11:37 PST 2009
//    I fixed a bug where points and lines were not deleted.
//
// ****************************************************************************

vtkPolyData *
avtFLASHFileFormat::GetMortonCurveSubset(int domain)
{
    vtkPolyData *pdata = vtkPolyData::New();
    vtkPoints *points = vtkPoints::New();
    vtkCellArray *lines = vtkCellArray::New();

    //
    // One cell per line segment, and unique end points (ones that coincide
    // are duplicated in vtkPoints)
    // Read centers of leaf blocks and insert into point object
    //

    //  LEAF-BLOCK MORTON CURVE
    vector<int>::iterator i = find(leafBlocks.begin(), leafBlocks.end(), domain);
    if (i != leafBlocks.end())  //  "domain" is in "leafBlocks"
    {
        if (i == leafBlocks.begin())
        {
            points->InsertPoint(0, blocks[domain].coords[0], blocks[domain].coords[1], blocks[domain].coords[2]);
            points->InsertPoint(1, blocks[*(i+1)].coords[0], blocks[*(i+1)].coords[1], blocks[*(i+1)].coords[2]);
            // Each cell is a (2-point) line segment
            lines->InsertNextCell(2);
            lines->InsertCellPoint(0);
            lines->InsertCellPoint(1);
        }
        else if (i == (leafBlocks.end()-1))
        {
            points->InsertPoint(0, blocks[*(i-1)].coords[0], blocks[*(i-1)].coords[1], blocks[*(i-1)].coords[2]);
            points->InsertPoint(1, blocks[domain].coords[0], blocks[domain].coords[1], blocks[domain].coords[2]);
            // Each cell is a (2-point) line segment
            lines->InsertNextCell(2);
            lines->InsertCellPoint(0);
            lines->InsertCellPoint(1);
        }
        else    //  "domain" is neither end block
        {
            // Interior points are duplicated so neighboring segments don't share them
            points->InsertPoint(0, blocks[*(i-1)].coords[0], blocks[*(i-1)].coords[1], blocks[*(i-1)].coords[2]);
            points->InsertPoint(1, blocks[domain].coords[0], blocks[domain].coords[1], blocks[domain].coords[2]);
            points->InsertPoint(2, blocks[domain].coords[0], blocks[domain].coords[1], blocks[domain].coords[2]);
            points->InsertPoint(3, blocks[*(i+1)].coords[0], blocks[*(i+1)].coords[1], blocks[*(i+1)].coords[2]);
            // Each cell is a (2-point) line segment
            lines->InsertNextCell(2);
            lines->InsertCellPoint(0);
            lines->InsertCellPoint(1);
            lines->InsertNextCell(2);
            lines->InsertCellPoint(2);
            lines->InsertCellPoint(3);
        }

        pdata->SetPoints(points);
        pdata->SetLines(lines);
    }
   
    points->Delete();
    lines->Delete();

    return pdata;
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::GetMortonCurve
//
//  Purpose:
//      Build and return the Morton space-filling curve as a vtkPolyData object.
//
//  Programmer: Randy Hudson
//  Creation:   April 3, 2007
//
//  Modifications:
//    Brad Whitlock, Wed Nov 18 11:11:37 PST 2009
//    I fixed a bug where points and lines were not deleted.
//
// ****************************************************************************

vtkPolyData *
avtFLASHFileFormat::GetMortonCurve()
{
    vtkPolyData *pdata = vtkPolyData::New();
    vtkPoints *points = vtkPoints::New();
    vtkCellArray *lines = vtkCellArray::New();
    int i, j;

    //
    // One cell per line segment, and unique end points (ones that coincide
    // are duplicated in vtkPoints)
    // Read centers of leaf blocks and insert into point object
    //
    for (i=0, j=0; i<numBlocks; i++)
    {
        if (blocks[i].nodetype == LEAF_NODE)
        {
            points->InsertPoint(j, blocks[i].coords[0], blocks[i].coords[1], blocks[i].coords[2]);
            j++;
            if (j!=1)
            {
                //
                // Interior points are duplicated so neighboring segments
                // don't share them
                //
                points->InsertPoint(j, blocks[i].coords[0], blocks[i].coords[1], blocks[i].coords[2]);
                j++;
            }
        }
    }
    for (i=0; i<(j-2); i+=2)
    {
        // Each cell is a (2-point) line; ignore duplicate of last point
        lines->InsertNextCell(2);
        lines->InsertCellPoint(i);
        lines->InsertCellPoint(i+1);
    }

    pdata->SetPoints(points);
    pdata->SetLines(lines);
    points->Delete();
    lines->Delete();

    return pdata;
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::GetVar
//
//  Purpose:
//      Gets a scalar variable associated with this file.  Although VTK has
//      support for many different types, the best bet is vtkFloatArray, since
//      that is supported everywhere through VisIt.
//
//  Arguments:
//      domain     The index of the domain.  If there are NDomains, this
//                 value is guaranteed to be between 0 and NDomains-1,
//                 regardless of block origin.
//      varname    The name of the variable requested.
//
//  Note: because the domains are small, we might get a speed boost by
//        leaving the varId and spaceId open for each variable, maybe even
//        caching things like the memspace
//
//  Programmer: Jeremy Meredith
//  Creation:   August 23, 2005
//
//  Modifications:
//    Jeremy Meredith, Thu Aug 25 15:07:36 PDT 2005
//    Added particle support.
//
//    Jeremy Meredith, Tue Sep 27 14:24:32 PDT 2005
//    Added "new" style particle support where the HDF5 variable name
//    containing particle data has changed.
//
//    Mark C. Miller, Thu Apr  6 17:06:33 PDT 2006
//    Added conditional compilation for hssize_t type
//
//    Randy Hudson, July 19, 2007
//    Added support for concurrent block-level and block-processor subset pairs
//      for both domain and morton curve meshes
//
//    Brad Whitlock, Wed Nov 18 11:14:16 PST 2009
//    Delete particle data arrays!
//
//    Hank Childs, Fri Dec 11 13:15:13 PST 2009
//    Add support for reordering of indices for SIL efficiencies.
//
// ****************************************************************************

vtkDataArray *
avtFLASHFileFormat::GetVar(int visitDomain, const char *vname)
{
    ReadAllMetaData();

    // Strip prefix (submenu name ("mesh_blockandproc/")) to leave actual var name
    string vn_str = vname;
    size_t pos = vn_str.find("/"); // position of "/" in str
    int theRealDomain = visitDomain;
    string vn_substr = vn_str;
    if (pos != string::npos)
        // We have a variable in a subdirectory.  Strip out the '/'
        vn_substr = vn_str.substr (pos+1); // get from just after "/" to the end
    else
        // We have a variable on the main mesh.  Convert its domain.
        theRealDomain = visitIdToFLASHId[visitDomain];


    if (particleOriginalIndexMap.count(vname))
    {
        //
        // It's a particle variable
        //
        int    index = particleOriginalIndexMap[vname];
        string varname = particleVarNames[index];
        hid_t  vartype = particleVarTypes[index];

        hid_t pointId = H5Dopen(fileId, particleHDFVarName.c_str());

        vtkFloatArray * fa = vtkFloatArray::New();
        fa->SetNumberOfTuples(numParticles);
        float *data = fa->GetPointer(0);

        if (vartype == H5T_NATIVE_DOUBLE)
        {
            double *ddata = new double[numParticles];
            if (fileFormatVersion < FLASH3_FFV8)
            {
                hid_t h5type = H5Tcreate(H5T_COMPOUND, sizeof(double));
                H5Tinsert(h5type, varname.c_str(), 0, H5T_NATIVE_DOUBLE);

                H5Dread(pointId, h5type, H5S_ALL,H5S_ALL,H5P_DEFAULT, ddata);
                H5Tclose(h5type);
            }
            else
            {
                ReadParticleVar(pointId, vname, ddata);
            }
            for (int i=0; i<numParticles; i++)
                data[i] = ddata[i];

            delete [] ddata;
        }
        else if (vartype == H5T_NATIVE_INT)
        {
            hid_t h5type = H5Tcreate(H5T_COMPOUND, sizeof(int));
            H5Tinsert(h5type, varname.c_str(), 0, H5T_NATIVE_INT);

            int *idata = new int[numParticles];
            H5Dread(pointId, h5type, H5S_ALL,H5S_ALL,H5P_DEFAULT, idata);

            for (int i=0; i<numParticles; i++)
                data[i] = idata[i];

            H5Tclose(h5type);
            delete [] idata;
        }
        else
        {
            EXCEPTION1(InvalidVariableException, varname);
        }

        H5Dclose(pointId);

        return fa;
    }
    else
    {
        //
        // It's a grid variable
        //

        hid_t varId = H5Dopen(fileId, vn_substr.c_str());
        if (varId < 0)
        {
            EXCEPTION1(InvalidVariableException, vn_substr.c_str());
        }

        hid_t spaceId = H5Dget_space(varId);

        hsize_t dims[4];
        hsize_t ndims = H5Sget_simple_extent_dims(spaceId, dims, NULL);

        if (ndims != 4)
        {
            EXCEPTION1(InvalidVariableException, vn_substr.c_str());
        }

        int ntuples = dims[1]*dims[2]*dims[3];  //dims[0]==numBlocks

        //
        // Set up a data space to read the right domain
        //
#if HDF5_VERSION_GE(1,6,4)
        hsize_t start[5];
#else
        hssize_t start[5];
#endif
        hsize_t stride[5], count[5];
    
        start[0]  = theRealDomain;
        start[1]  = 0;
        start[2]  = 0;
        start[3]  = 0;
    
        stride[0] = 1;
        stride[1] = 1;
        stride[2] = 1;
        stride[3] = 1;
    
        count[0]  = 1;
        count[1]  = dims[1];
        count[2]  = dims[2];
        count[3]  = dims[3];
    
        hid_t dataspace = H5Screate_simple(4, dims, NULL);
        H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, NULL);

        start[0]  = 0;
        start[1]  = 0;
        start[2]  = 0;
        start[3]  = 0;
    
        stride[0] = 1;
        stride[1] = 1;
        stride[2] = 1;
        stride[3] = 1;
    
        count[0]  = 1;
        count[1]  = dims[1];
        count[2]  = dims[2];
        count[3]  = dims[3];
    
        hid_t memspace = H5Screate_simple(4, dims, NULL);
        H5Sselect_hyperslab(memspace, H5S_SELECT_SET, start, stride, count, NULL);

        vtkFloatArray * fa = vtkFloatArray::New();
        fa->SetNumberOfTuples(ntuples);
        float *data = fa->GetPointer(0);

        double *d_data;
        int  *i_data;
        unsigned int *ui_data;
        int i;

        hid_t raw_data_type = H5Dget_type(varId);
        hid_t data_type = H5Tget_native_type(raw_data_type, H5T_DIR_ASCEND);
        if (H5Tequal(data_type, H5T_NATIVE_FLOAT)>0)
        {
            H5Dread(varId, data_type,memspace,dataspace,H5P_DEFAULT, data);
        }
        else if (H5Tequal(data_type, H5T_NATIVE_DOUBLE)>0)
        {
            d_data = new double[ntuples];
            H5Dread(varId, data_type,memspace,dataspace,H5P_DEFAULT, d_data);
            for (i = 0 ; i < ntuples ; i++)
                data[i] = d_data[i];
            delete[] d_data;
        }
        else if (H5Tequal(data_type, H5T_NATIVE_INT))
        {
            i_data = new int[ntuples];
            H5Dread(varId, data_type,memspace,dataspace,H5P_DEFAULT, i_data);
            for (i = 0 ; i < ntuples ; i++)
                data[i] = i_data[i];
            delete[] i_data;
        }
        else if (H5Tequal(data_type, H5T_NATIVE_UINT))
        {
            ui_data = new unsigned int[ntuples];
            H5Dread(varId, data_type,memspace,dataspace,H5P_DEFAULT, ui_data);
            for (i = 0 ; i < ntuples ; i++)
                data[i] = ui_data[i];
            delete[] ui_data;
        }
        else
        {
            // ERROR: UKNOWN TYPE
            EXCEPTION1(InvalidVariableException, vn_substr.c_str());
        }

        // Done with hyperslab
        H5Sclose(dataspace);

        // Done with the space
        H5Sclose(spaceId);

        // Done with the type
        H5Tclose(data_type);
        H5Tclose(raw_data_type);

        // Done with the variable; don't leak it
        H5Dclose(varId);

        return fa;
    }
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::GetVectorVar
//
//  Purpose:
//      Gets a vector variable associated with this file.  Although VTK has
//      support for many different types, the best bet is vtkFloatArray, since
//      that is supported everywhere through VisIt.
//
//  Arguments:
//      domain     The index of the domain.  If there are NDomains, this
//                 value is guaranteed to be between 0 and NDomains-1,
//                 regardless of block origin.
//      varname    The name of the variable requested.
//
//  Programmer: Jeremy Meredith
//  Creation:   August 23, 2005
//
//  Modifications:
//
// ****************************************************************************

vtkDataArray *
avtFLASHFileFormat::GetVectorVar(int visitDomain, const char *varname)
{
    // Is this necessary?  No.  But I don't want someone to get caught if
    // they ever decide to implement this method.
    //   int domain = visitIdToFLASHId[visitDomain];
    return NULL;
}


// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadAllMetaData
//
//  Purpose:
//    Read the metadata if we have not done so yet.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
//  Modifications:
//    Jeremy Meredith, Thu Aug 25 15:07:36 PDT 2005
//    Added particle support.
//
//    Jeremy Meredith, Tue Sep 27 14:24:45 PDT 2005
//    Added support for files containing only particles, and no grids.
//
//    Randy Hudson, Apr 4, 2007
//    Added call to ReadNodeTypes.
//    Added call to ReadCoordinates.
//
//    Randy Hudson, June 12, 2007
//    Added call to ReadProcessorNumbers.
//
//    Hank Childs, Tue Dec 15 14:02:40 PST 2009
//    Calculate some data members here when we read the blocks.
//
//    Jeremy Meredith, Thu Jan  7 15:36:19 EST 2010
//    Close all open ids when returning an exception.
//
//    Andrew Szymkowiak, Wed Feb 23 22:32:06 PST 2011
//    Zero out patchesPerLevel vector so we don't miscount and end up with
//    SIL generation errors.
//
// ****************************************************************************

void
avtFLASHFileFormat::ReadAllMetaData()
{

    if (fileId >= 0)
    {
        return;
    }
    
    fileId = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
    if (fileId < 0)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    ReadVersionInfo(fileId);

    if (fileFormatVersion < FLASH3_FFV8)
    {
        ReadParticleAttributes(); // FLASH2 version
    }
    else 
    {
        ReadParticleAttributes_FLASH3(); // FLASH3 version
    }

    ReadBlockStructure();

    if (numParticles == 0 && numBlocks == 0)
    {
        H5Fclose(fileId);
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    if (numBlocks > 0)
    {
        ReadBlockExtents();
        ReadRefinementLevels();
        ReadSimulationParameters(fileId);
        ReadUnknownNames();
        DetermineGlobalLogicalExtentsForAllBlocks();
        ReadNodeTypes();
        ReadCoordinates();
        ReadProcessorNumbers();

        patchesPerLevel.resize(numLevels);
        memset(&patchesPerLevel[0], 0, numLevels * sizeof(int));
        int  i;

        for (i = 0; i < numBlocks; i++)
             patchesPerLevel[blocks[i].level-1]++;
        
        vector<int> numToThisPoint(numLevels);
        numToThisPoint[0] = 0;
        for (i = 1 ; i < numLevels ; i++)
            numToThisPoint[i] = numToThisPoint[i-1] + patchesPerLevel[i-1];

        visitIdToFLASHId.resize(numBlocks, -1);
        vector<int> numForThisLevel(numLevels, 0);
        for (i = 0 ; i < numBlocks ; i++)
        {
             int level = blocks[i].level-1;
             int visitIdx = numToThisPoint[level] + numForThisLevel[level]++;
             visitIdToFLASHId[visitIdx] = i;
        }

        FLASHIdToVisitId.resize(numBlocks, -1);
        for (i = 0 ; i < numBlocks ; i++)
        {
             FLASHIdToVisitId[visitIdToFLASHId[i]] = i;
        }
    }
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::ReadProcessorNumbers
//
//  Purpose:
//      Read the ID's of the processors the blocks were processed on
//
//  Programmer: Randy Hudson
//  Creation:   June 12, 2007
//
//  Modifications:
//    Randy Hudson, Apr 4, 2007
//    Added support for (old) files w/o "processor number".
//
//    Jeremy Meredith, Thu Jan  7 15:36:19 EST 2010
//    Close all open ids when returning an exception.
//
// ****************************************************************************

// Support for files w/o "processor number"
void avtFLASHFileFormat::ReadProcessorNumbers()
{
    hid_t rootId = H5Gopen(fileId, "/");
    if (rootId < 0)
    {
        debug5 << "[avtFLASHFileFormat::ReadProcessorNumbers] - Didn't open root group" << endl;
        H5Fclose(fileId);
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }
    hsize_t num_obj;
    herr_t errId = H5Gget_num_objs(rootId, &num_obj);
    if (errId < 0)
    {
        debug5 << "[avtFLASHFileFormat::ReadProcessorNumbers] - Can't get # of objects in root group" << endl;
        H5Gclose(rootId);
        H5Fclose(fileId);
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }
    hsize_t idx;
    string objname = "processor number";
    char namefromfile[17];
    for (idx=0; idx<num_obj; idx++)
    {
       ssize_t objsize = H5Gget_objname_by_idx(rootId, idx, NULL, 0);
       if (objsize == 16)
       {
           ssize_t objsize = H5Gget_objname_by_idx(rootId, idx, namefromfile, 17); (void) objsize;
           string tempstr = namefromfile;
           if (tempstr == objname)  //  If this file contains processor numbers
           {
               file_has_procnum = true;
           }
       }
    }
    H5Gclose(rootId);

    if (file_has_procnum)
    {
        //
        // Read the processor number description for the blocks
        //
        hid_t procnumId = H5Dopen(fileId, "processor number");
        if (procnumId < 0)
        {
            H5Fclose(fileId);
            EXCEPTION1(InvalidFilesException, filename.c_str());
        }

        hid_t procnumSpaceId = H5Dget_space(procnumId);
    
        hsize_t procnum_dims[1];
        hsize_t procnum_ndims = H5Sget_simple_extent_dims(procnumSpaceId,
                                                          procnum_dims,NULL);

        if (procnum_ndims != 1 || procnum_dims[0] != (hsize_t)numBlocks)
        {
            EXCEPTION1(InvalidFilesException, filename.c_str());
        }

        hid_t procnum_raw_data_type = H5Dget_type(procnumId);
        hid_t procnum_data_type = H5Tget_native_type(procnum_raw_data_type,
                                                     H5T_DIR_ASCEND);
    
        int *procnum_array = new int[numBlocks];
        H5Dread(procnumId, procnum_data_type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                procnum_array);

        //  numProcessors = 0;
        int highProcessor = -1;
        for (int b=0; b<numBlocks; b++)
        {
            int pnum = procnum_array[b];
            if (pnum > highProcessor) {
                highProcessor = pnum;
                //          numProcessors += pnum;
                numProcessors++;
            }
            blocks[b].procnum = pnum;
        }

        // Done with the type
        H5Tclose(procnum_data_type);
        H5Tclose(procnum_raw_data_type);

        // Done with the space
        H5Sclose(procnumSpaceId);

        // Done with the variable; don't leak it
        H5Dclose(procnumId);

        // Delete the raw array
        delete[] procnum_array;
    }
    else
    {
        numProcessors = 1;
        for (int b=0; b<numBlocks; b++)
        {
            blocks[b].procnum = 0;
        }
    }
//  //  Use EXCEPTION1 as clean exit after above test:
//  EXCEPTION1(InvalidFilesException, filename.c_str());

}


// ****************************************************************************
//  Method: avtFLASHFileFormat::ReadCoordinates
//
//  Purpose:
//      Read coordinates of centers of blocks.
//
//  Programmer: Randy Hudson
//  Creation:   April 4, 2007
//
//  Changes:
//    Randy Hudson, February 11, 2008
//    Changed code to distinguish between file format versions 8 and 9.
//
// ****************************************************************************
void avtFLASHFileFormat::ReadCoordinates()
{
    //
    // Read the coordinates description for the blocks
    //
    hid_t coordinatesId = H5Dopen(fileId, "coordinates");
    if (coordinatesId < 0)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t coordinatesSpaceId = H5Dget_space(coordinatesId);

    hsize_t coordinates_dims[2];
    hsize_t coordinates_ndims = H5Sget_simple_extent_dims(coordinatesSpaceId, coordinates_dims, NULL);

    if (fileFormatVersion <= FLASH3_FFV8)
    {
        if (coordinates_ndims != 2 ||
            coordinates_dims[0] != (hsize_t)numBlocks ||
            coordinates_dims[1] != (hsize_t)dimension)
        {
            EXCEPTION1(InvalidFilesException, filename.c_str());
        }

        double *coordinates_array = new double[numBlocks * dimension];
        H5Dread(coordinatesId, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coordinates_array);

        for (int b=0; b<numBlocks; b++)
        {
             double *coords = &coordinates_array[dimension*b];
             if (dimension == 1)
             {
                 blocks[b].coords[0] = coords[0];
                 blocks[b].coords[1] = 0.0;
                 blocks[b].coords[2] = 0.0;
             }
             else if (dimension == 2)
             {
                 blocks[b].coords[0] = coords[0];
                 blocks[b].coords[1] = coords[1];
                 blocks[b].coords[2] = 0.0;
             }
             else if (dimension == 3)
             {
                 blocks[b].coords[0] = coords[0];
                 blocks[b].coords[1] = coords[1];
                 blocks[b].coords[2] = coords[2];
             }
        }
        // Delete the raw array
        delete [] coordinates_array;
    }
    else if (fileFormatVersion == FLASH3_FFV9)
    {
        if (coordinates_ndims != 2 ||
            coordinates_dims[0] != (hsize_t)numBlocks ||
            coordinates_dims[1] != (hsize_t)MDIM)
        {
            EXCEPTION1(InvalidFilesException, filename.c_str());
        }

        double *coordinates_array = new double[numBlocks * MDIM];
        H5Dread(coordinatesId, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coordinates_array);

        for (int b=0; b<numBlocks; b++)
        {
             double *coords = &coordinates_array[MDIM*b];
             blocks[b].coords[0] = coords[0];
             blocks[b].coords[1] = coords[1];
             blocks[b].coords[2] = coords[2];
        }
        // Delete the raw array
        delete[] coordinates_array;
    }

    // Done with the space
    H5Sclose(coordinatesSpaceId);

    // Done with the variable; don't leak it
    H5Dclose(coordinatesId);
}


// ****************************************************************************
//  Method: avtFLASHFileFormat::ReadNodeTypes
//
//  Purpose:
//      Read node types of blocks and count the leaf blocks ( of node type '1')
//
//  Programmer: Randy Hudson
//  Creation:   April 4, 2007
//
//  Changes:
//    Randy Hudson, June 23, 2007
//    Added code to build the vector of leaf blocks for subsets of the Morton curve.
//
// ****************************************************************************

void avtFLASHFileFormat::ReadNodeTypes()
{
    //
    // Read the node type description for the blocks
    //
    hid_t nodetypeId = H5Dopen(fileId, "node type");
    if (nodetypeId < 0)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t nodetypeSpaceId = H5Dget_space(nodetypeId);
    
    hsize_t nodetype_dims[1];
    hsize_t nodetype_ndims = H5Sget_simple_extent_dims(nodetypeSpaceId,
                                                         nodetype_dims,NULL);

    if (nodetype_ndims != 1 || nodetype_dims[0] != (hsize_t)numBlocks)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t nodetype_raw_data_type = H5Dget_type(nodetypeId);
    hid_t nodetype_data_type = H5Tget_native_type(nodetype_raw_data_type,
                                                    H5T_DIR_ASCEND);
    
    int *nodetype_array = new int[numBlocks];
    H5Dread(nodetypeId, nodetype_data_type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
            nodetype_array);

    numLeafBlocks = 0;
    for (int b=0; b<numBlocks; b++)
    {
        int ntype = nodetype_array[b];
        blocks[b].nodetype = ntype;
        if (ntype == LEAF_NODE)
        {
            numLeafBlocks++;
            leafBlocks.push_back(b);
        }
    }

    // Done with the type
    H5Tclose(nodetype_data_type);
    H5Tclose(nodetype_raw_data_type);

    // Done with the space
    H5Sclose(nodetypeSpaceId);

    // Done with the variable; don't leak it
    H5Dclose(nodetypeId);

    // Delete the raw array
    delete[] nodetype_array;
}


// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadBlockStructure
//
//  Purpose:
//    Read the domain connectivity and hierarchy.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
//  Modifications:
//    Jeremy Meredith, Tue Sep 27 14:25:02 PDT 2005
//    Let this function fail silently; some FLASH files contain only
//    particles and no grids, and we want to support those without errors.
//
// ****************************************************************************

void avtFLASHFileFormat::ReadBlockStructure()
{
    // temporarily disable error reporting
    H5E_auto_t  old_errorfunc;
    void       *old_clientdata;
    H5Eget_auto(&old_errorfunc, &old_clientdata);
    H5Eset_auto(NULL, NULL);

    //
    // Read the "gid" block connectivity description
    //
    hid_t gidId = H5Dopen(fileId, "gid");

    // turn back on error reporting
    H5Eset_auto(old_errorfunc, old_clientdata);

    if (gidId < 0)
    {
        numBlocks = 0;
        return;
    }

    hid_t gidSpaceId = H5Dget_space(gidId);
    
    hsize_t gid_dims[2];
    hsize_t gid_ndims =  H5Sget_simple_extent_dims(gidSpaceId, gid_dims, NULL);
    if (gid_ndims != 2)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    numBlocks = gid_dims[0];
    switch (gid_dims[1])
    {
      case 5:
        dimension = 1;
        numChildrenPerBlock = 2;
        numNeighborsPerBlock = 2;
        break;
      case 9:
        dimension = 2;
        numChildrenPerBlock = 4;
        numNeighborsPerBlock = 4;
        break;
      case 15:
        dimension = 3;
        numChildrenPerBlock = 8;
        numNeighborsPerBlock = 6;
        break;
      default:
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t gid_raw_data_type = H5Dget_type(gidId);
    hid_t gid_data_type = H5Tget_native_type(gid_raw_data_type,H5T_DIR_ASCEND);
    
    int *gid_array = new int[numBlocks * gid_dims[1]];
    H5Dread(gidId, gid_data_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, gid_array);

    // convert to an easier-to-grok format
    blocks.resize(numBlocks);
    for (int b=0; b<numBlocks; b++)
    {
        int *gid_line = &gid_array[gid_dims[1]*b];
        int  pos=0;

        blocks[b].ID = b+1;  // 1-origin IDs
        for (int n=0; n<numNeighborsPerBlock; n++)
        {
            blocks[b].neighborIDs[n] = gid_line[pos++];
        }
        blocks[b].parentID = gid_line[pos++];
        for (int n=0; n<numChildrenPerBlock; n++)
        {
            blocks[b].childrenIDs[n] = gid_line[pos++];
        }
    }

    // Done with the type
    H5Tclose(gid_data_type);
    H5Tclose(gid_raw_data_type);

    // Done with the space
    H5Sclose(gidSpaceId);

    // Done with the variable; don't leak it
    H5Dclose(gidId);

    // Delete the raw array
    delete[] gid_array;
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadBlockExtents
//
//  Purpose:
//    Read the spatial extents for the blocks.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
//  Modifications:
//    Jeremy Meredith, Tue Sep 27 14:26:41 PDT 2005
//    Force read data type to double; in other words, don't assume it was
//    saved as double precision values.
//
//    Randy Hudson, February 11, 2008
//    Changed code to distinguish between file format versions 8 and 9.
//
// ****************************************************************************
void avtFLASHFileFormat::ReadBlockExtents()
{
    //
    // Read the bounding box description for the blocks
    //
    hid_t bboxId = H5Dopen(fileId, "bounding box");
    if (bboxId < 0)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t bboxSpaceId = H5Dget_space(bboxId);
    
    hsize_t bbox_dims[3];
    hsize_t bbox_ndims = H5Sget_simple_extent_dims(bboxSpaceId, bbox_dims, NULL);

    if (fileFormatVersion <= FLASH3_FFV8)
    {
        if (bbox_ndims != 3 ||
            bbox_dims[0] != (hsize_t)numBlocks ||
            bbox_dims[1] != (hsize_t)dimension ||
            bbox_dims[2] != 2)
        {
            EXCEPTION1(InvalidFilesException, filename.c_str());
        }

        double *bbox_array = new double[numBlocks * dimension * 2];
        H5Dread(bboxId, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, bbox_array);
    
        minSpatialExtents[0] = FLT_MAX;
        minSpatialExtents[1] = FLT_MAX;
        minSpatialExtents[2] = FLT_MAX;
        maxSpatialExtents[0] = -FLT_MAX;
        maxSpatialExtents[1] = -FLT_MAX;
        maxSpatialExtents[2] = -FLT_MAX;
    
        for (int b=0; b<numBlocks; b++)
        {
            double *bbox_line = &bbox_array[dimension*2*b];
            for (int d=0; d<3; d++)
            {
                if (d+1 <= dimension)
                {
                    blocks[b].minSpatialExtents[d] = bbox_line[d*2 + 0];
                    blocks[b].maxSpatialExtents[d] = bbox_line[d*2 + 1];
                }
                else
                {
                    blocks[b].minSpatialExtents[d] = 0;
                    blocks[b].maxSpatialExtents[d] = 0;
                }
    
                if (blocks[b].minSpatialExtents[d] < minSpatialExtents[d])
                    minSpatialExtents[d] = blocks[b].minSpatialExtents[d];
    
                if (blocks[b].maxSpatialExtents[d] > maxSpatialExtents[d])
                    maxSpatialExtents[d] = blocks[b].maxSpatialExtents[d];
            }
        }
        // Delete the raw array
        delete[] bbox_array;
    }
    else if (fileFormatVersion == FLASH3_FFV9)
    {
        if (bbox_ndims != 3 ||
            bbox_dims[0] != (hsize_t)numBlocks ||
            bbox_dims[1] != (hsize_t)MDIM ||
            bbox_dims[2] != 2)
        {
            EXCEPTION1(InvalidFilesException, filename.c_str());
        }
    
        double *bbox_array = new double[numBlocks * MDIM * 2];
        H5Dread(bboxId, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, bbox_array);
    
        minSpatialExtents[0] = FLT_MAX;
        minSpatialExtents[1] = FLT_MAX;
        minSpatialExtents[2] = FLT_MAX;
        maxSpatialExtents[0] = -FLT_MAX;
        maxSpatialExtents[1] = -FLT_MAX;
        maxSpatialExtents[2] = -FLT_MAX;
    
        for (int b=0; b<numBlocks; b++)
        {
            double *bbox_line = &bbox_array[MDIM*2*b];
            for (int d=0; d<3; d++)
            {
                blocks[b].minSpatialExtents[d] = bbox_line[d*2 + 0];
                blocks[b].maxSpatialExtents[d] = bbox_line[d*2 + 1];
    
                if (blocks[b].minSpatialExtents[d] < minSpatialExtents[d])
                    minSpatialExtents[d] = blocks[b].minSpatialExtents[d];
    
                if (blocks[b].maxSpatialExtents[d] > maxSpatialExtents[d])
                    maxSpatialExtents[d] = blocks[b].maxSpatialExtents[d];
            }
        }    
        // Delete the raw array
        delete[] bbox_array;
    }

    // Done with the space
    H5Sclose(bboxSpaceId);

    // Done with the variable; don't leak it
    H5Dclose(bboxId);
}


// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadRefinementLevels
//
//  Purpose:
//    Read the explicit refinement levels for the blocks.  We could
//    theoretically guess it based on size, but it's much cleaner and more
//    robust to simply read it from the file and use it as fact.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
// ****************************************************************************
void avtFLASHFileFormat::ReadRefinementLevels()
{
    //
    // Read the bounding box description for the blocks
    //
    hid_t refinementId = H5Dopen(fileId, "refine level");
    if (refinementId < 0)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t refinementSpaceId = H5Dget_space(refinementId);
    
    hsize_t refinement_dims[1];
    hsize_t refinement_ndims = H5Sget_simple_extent_dims(refinementSpaceId,
                                                         refinement_dims,NULL);

    if (refinement_ndims != 1 || refinement_dims[0] != (hsize_t)numBlocks)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t refinement_raw_data_type = H5Dget_type(refinementId);
    hid_t refinement_data_type = H5Tget_native_type(refinement_raw_data_type,
                                                    H5T_DIR_ASCEND);
    
    int *refinement_array = new int[numBlocks];
    H5Dread(refinementId, refinement_data_type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
            refinement_array);

    for (int b=0; b<numBlocks; b++)
    {
        int level = refinement_array[b];
        blocks[b].level = level;
        if (level > numLevels)
        {
            numLevels = level;
        }
    }

    // Done with the type
    H5Tclose(refinement_data_type);
    H5Tclose(refinement_raw_data_type);

    // Done with the space
    H5Sclose(refinementSpaceId);

    // Done with the variable; don't leak it
    H5Dclose(refinementId);

    // Delete the raw array
    delete[] refinement_array;
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadSimulationParameters
//
//  Purpose:
//    Read the simulation parameters from the file.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
//  Modifications:
//    Jeremy Meredith, Tue Sep 27 14:28:01 PDT 2005
//    Made the read of the simulation parameters more arbitrary; different
//    flavors of FLASH files have stored the data members in different
//    order or as different data types, and thus we can't assume a single
//    data structure.
//
//    Kathleen Bonnell, Thu Jul 20 11:22:13 PDT 2006
//    Added support for FLASH3 file versions.
//
//    Mark C. Miller, Tue Mar  6 23:41:33 PST 2007
//    Added bool for reading just enough to get cycle/time info
//
// ****************************************************************************
void avtFLASHFileFormat::ReadSimulationParameters(hid_t file_id,
    bool timeAndCycleOnly)
{
    if (fileFormatVersion < FLASH3_FFV8)
    {
        //
        // Read the simulation parameters
        //
        hid_t simparamsId = H5Dopen(file_id, "simulation parameters");
        if (simparamsId < 0)
        {
            EXCEPTION1(InvalidFilesException, filename.c_str());
        }

        hid_t sp_type = H5Tcreate(H5T_COMPOUND, sizeof(SimParams));
        H5Tinsert(sp_type, "total blocks",   HOFFSET(SimParams, total_blocks), H5T_NATIVE_INT);
        H5Tinsert(sp_type, "time",           HOFFSET(SimParams, time),         H5T_NATIVE_DOUBLE);
        H5Tinsert(sp_type, "timestep",       HOFFSET(SimParams, timestep),     H5T_NATIVE_DOUBLE);
        H5Tinsert(sp_type, "redshift",       HOFFSET(SimParams, redshift),     H5T_NATIVE_DOUBLE);
        H5Tinsert(sp_type, "number of steps",HOFFSET(SimParams, nsteps),       H5T_NATIVE_INT);
        H5Tinsert(sp_type, "nxb",            HOFFSET(SimParams, nxb),          H5T_NATIVE_INT);
        H5Tinsert(sp_type, "nyb",            HOFFSET(SimParams, nyb),          H5T_NATIVE_INT);
        H5Tinsert(sp_type, "nzb",            HOFFSET(SimParams, nzb),          H5T_NATIVE_INT);

        H5Dread(simparamsId, sp_type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
            &simParams);

        // Done with the type
        H5Tclose(sp_type);

        // Done with the variable; don't leak it
        H5Dclose(simparamsId);
    }
    else
    {
        ReadIntegerScalars(file_id);
        ReadRealScalars(file_id);
    }

    if (timeAndCycleOnly)
        return;

    // Sanity check: size of the gid array better match number of blocks
    //               reported in the simulation parameters
    if (simParams.total_blocks != numBlocks)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    if (simParams.nxb == 1)
    {
        block_ndims[0] = 1;
        block_zdims[0] = 1;
    }
    else
    {
        block_ndims[0] = simParams.nxb+1;
        block_zdims[0] = simParams.nxb;
    }

    if (simParams.nyb == 1)
    {
        block_ndims[1] = 1;
        block_zdims[1] = 1;
    }
    else
    {
        block_ndims[1] = simParams.nyb+1;
        block_zdims[1] = simParams.nyb;
    }

    if (simParams.nzb == 1)
    {
        block_ndims[2] = 1;
        block_zdims[2] = 1;
    }
    else
    {
        block_ndims[2] = simParams.nzb+1;
        block_zdims[2] = simParams.nzb;
    }
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadUnknownNames
//
//  Purpose:
//    Read the variable name list.  They are called "unknowns" in
//    FLASH terminology.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
//  Modifications:
//    Brad Whitlock, Wed Nov 18 11:26:09 PST 2009
//    Delete some arrays.
//
// ****************************************************************************

void
avtFLASHFileFormat::ReadUnknownNames()
{
    //
    // Read the variable ("unknown") names
    //
    hid_t unknownsId = H5Dopen(fileId, "unknown names");
    if (unknownsId < 0)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t unkSpaceId = H5Dget_space(unknownsId);
    
    hsize_t unk_dims[2];
    hsize_t unk_ndims =  H5Sget_simple_extent_dims(unkSpaceId, unk_dims, NULL);
    if (unk_ndims != 2 || unk_dims[1] != 1)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t unk_raw_data_type = H5Dget_type(unknownsId);
    int length = H5Tget_size(unk_raw_data_type);

    int nvars = unk_dims[0];
    char *unk_array = new char[nvars * length];

    H5Dread(unknownsId, unk_raw_data_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, unk_array);

    varNames.resize(nvars);
    char *tmpstring = new char[length+1];
    for (int v=0; v<nvars; v++)
    {
        for (int c=0; c<length; c++)
        {
            tmpstring[c] = unk_array[v*length + c];
        }
        tmpstring[length] = '\0';

        varNames[v] = tmpstring;
    }

    delete [] unk_array;
    delete [] tmpstring;

    // Done with the type
    H5Tclose(unk_raw_data_type);

    // Done with the space
    H5Sclose(unkSpaceId);

    // Done with the variable; don't leak it
    H5Dclose(unknownsId);
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadParticleAttributes
//
//  Purpose:
//    Read the particle attributes, like number of particles and
//    variable names.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 25, 2005
//
//  Modifications:
//    Jeremy Meredith, Tue Sep 27 14:29:42 PDT 2005
//    Added "new" style particle support where the HDF5 variable name
//    containing particle data has changed.  It turns out the data structure
//    itself has also changed, but we are reading its contents in a robust
//    enough fashion that this didn't bite us.  Also, added support for
//    FLASH files containing only particles and no grid data.
//
//    Brad Whitlock, Tue Nov 15 10:33:55 PDT 2005
//    I increased the size of a dimension so it will build on AIX.
//
// ****************************************************************************
void
avtFLASHFileFormat::ReadParticleAttributes()
{
    // temporarily disable error reporting
    H5E_auto_t  old_errorfunc;
    void       *old_clientdata;
    H5Eget_auto(&old_errorfunc, &old_clientdata);
    H5Eset_auto(NULL, NULL);

    // find the particle variable (if it exists)
    hid_t pointId;
    particleHDFVarName = "particle tracers";
    pointId = H5Dopen(fileId, particleHDFVarName.c_str());
    if (pointId < 0)
    {
        particleHDFVarName = "tracer particles";
        pointId = H5Dopen(fileId, particleHDFVarName.c_str());
    }

    // turn back on error reporting
    H5Eset_auto(old_errorfunc, old_clientdata);

    // Doesn't exist?  No problem -- we just don't have any particles
    if (pointId < 0)
    {
        numParticles = 0;
        return;
    }

    hid_t pointSpaceId = H5Dget_space(pointId);

    hsize_t p_dims[100];
    hsize_t p_ndims =  H5Sget_simple_extent_dims(pointSpaceId, p_dims, NULL);
    if (p_ndims != 1)
    {
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    numParticles = p_dims[0];

    hid_t point_raw_type = H5Dget_type(pointId);
    int numMembers = H5Tget_nmembers(point_raw_type);
    for (int i=0; i<numMembers; i++)
    {
        char  *member_name = H5Tget_member_name(point_raw_type, i);
        string nice_name = GetNiceParticleName(member_name);
        hid_t  member_raw_type = H5Tget_member_type(point_raw_type, i);
        hid_t  member_type = H5Tget_native_type(member_raw_type, H5T_DIR_ASCEND);
        int    index = particleVarTypes.size();
        if (H5Tequal(member_type, H5T_NATIVE_DOUBLE)>0)
        {
            particleVarTypes.push_back(H5T_NATIVE_DOUBLE);
            particleVarNames.push_back(member_name);
            particleOriginalIndexMap[nice_name] = index;
        }
        else if (H5Tequal(member_type, H5T_NATIVE_INT)>0)
        {
            particleVarTypes.push_back(H5T_NATIVE_INT);
            particleVarNames.push_back(member_name);
            particleOriginalIndexMap[nice_name] = index;
        }
        else
        {
            // only support double and int for now
        }

        // We read the particles before the grids.  Just in case we
        // don't have any grids, take a stab at the problem dimension
        // based purely on the existence of various data members.
        // This will be overwritten by the true grid topological
        // dimension if the grid exists.
        if (strcmp(member_name, "particle_x")==0 && dimension < 1)
            dimension = 1;
        if (strcmp(member_name, "particle_y")==0 && dimension < 2)
            dimension = 2;
        if (strcmp(member_name, "particle_z")==0 && dimension < 3)
            dimension = 3;

        H5Tclose(member_type);
        H5Tclose(member_raw_type);
    }

    H5Tclose(point_raw_type);
    H5Sclose(pointSpaceId);
    H5Dclose(pointId);
}


// ****************************************************************************
//  Method:  avtFLASHFileFormat::DetermineGlobalLogicalExtentsForAllBlocks
//
//  Purpose:
//    Get the global logical extents for this block at this refinement level.
//    This is needed for domain nesting and relies on all the block
//    extents and simulation parameters having been read.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
//  Modifications:
//    Jeremy Meredith, Tue Sep 27 14:30:59 PDT 2005
//    The old logic was failing when the origin of the data was not at
//    (0,0,0), and also when there was more than one top-level block.
//    Rewrote this routine to fix both these problems.
//
// ****************************************************************************
void avtFLASHFileFormat::DetermineGlobalLogicalExtentsForAllBlocks()
{
    double problemsize[3] = {maxSpatialExtents[0] - minSpatialExtents[0],
                             maxSpatialExtents[1] - minSpatialExtents[1],
                             maxSpatialExtents[2] - minSpatialExtents[2]};
    for (int b=0; b<numBlocks; b++)
    {
        Block &B = blocks[b];

        for (int d=0; d<3; d++)
        {
            if (d < dimension)
            {
                double factor = problemsize[d] / (B.maxSpatialExtents[d] - B.minSpatialExtents[d]);
                double start  = (B.minSpatialExtents[d] - minSpatialExtents[d]) / problemsize[d];

                double beg = (start * block_zdims[d] * factor);
                double end = (start * block_zdims[d] * factor) + block_zdims[d];
                blocks[b].minGlobalLogicalExtents[d] = int(beg+.5);
                blocks[b].maxGlobalLogicalExtents[d] = int(end+.5);
            }
            else
            {
                blocks[b].minGlobalLogicalExtents[d] = 0;
                blocks[b].maxGlobalLogicalExtents[d] = 0;
            }
        }
    }
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::BuildDomainNesting
//
//  Purpose:
//     Generates the domain nesting object needed to remove coarse zones in
//     an AMR mesh.
//
//  Arguments:
//    none
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 24, 2005
//
//  Modifications:
//    Jeremy Meredith, Tue Sep 27 14:31:56 PDT 2005
//    Made an indexing origin error for the domain boundaries.
//
//    Randy Hudson, Jul 29, 2008
//    Changed the hard-coded mesh name in two cache calls from "mesh" to
//    "mesh_blockandlevel" to match the new mesh name assigned in
//    "PopulateDatabaseMetaData()", then duplicated the contents of 
//    "BuildDomainNesting()" to process mesh "mesh_blockandproc", also assigned
//    in "PopulateDatabaseMetaData()".
//
//    Hank Childs, Tue Dec 15 14:30:07 PST 2009
//    Reorder indices to accommodate reordering of patches for SIL efficiency.
//
//    Hank Childs, Thu Dec 17 14:07:52 PST 2009
//    Added database options (for toggling between processors or levels).
//
//    Hank Childs, Sat Mar 20 20:25:14 PDT 2010
//    Only do domain abutment based on database option.
//
//    Gunther H. Weber, Mon Jul 28 18:14:55 PDT 2014
//    Add metdata required for AMRStitchCell operator
//
// ****************************************************************************

void
avtFLASHFileFormat::BuildDomainNesting()
{
    if (numBlocks <= 1 || avtDatabase::OnlyServeUpMetaData())
        return;

    //  ***********************************************************************
    //  PROCESS THE "amr_mesh" MESH
    //  ***********************************************************************

    // first, look to see if we don't already have it cached
    void_ref_ptr vrTmp = cache->GetVoidRef("amr_mesh",
                                   AUXILIARY_DATA_DOMAIN_NESTING_INFORMATION,
                                   timestep, -1);

    if ((*vrTmp == NULL))
    {
        int i;

        //
        // build the avtDomainNesting object
        //
        vector< vector<int> > refinement_ratios;

        if (numLevels > 0)
        {
            int t2 = visitTimer->StartTimer();
            avtStructuredDomainNesting *dn =
                new avtStructuredDomainNesting(numBlocks, numLevels);

            dn->SetNumDimensions(dimension);

            //
            // Set refinement level ratio information
            //

            // NOTE: FLASH files always have a 2:1 ratio
            vector<int> ratios(3);
            ratios[0] = 1;
            ratios[1] = 1;
            ratios[2] = 1;
            dn->SetLevelRefinementRatios(0, ratios);
            for (i = 1; i < numLevels; i++)
            {
                vector<int> ratios(3);
                ratios[0] = 2;
                ratios[1] = 2;
                ratios[2] = 2;
                dn->SetLevelRefinementRatios(i, ratios);
                refinement_ratios.push_back(ratios);
            }

            //
            // set each domain's level, children and logical extents
            //
            for (i = 0; i < numBlocks; i++)
            {
                vector<int> childBlocks;
                for (int j = 0; j < numChildrenPerBlock; j++)
                {
                    // if this is allowed to be 1-origin, the "-1" here
                    // needs to be removed
                    if (blocks[i].childrenIDs[j] >= 0)
                        childBlocks.push_back(FLASHIdToVisitId[blocks[i].childrenIDs[j] - 1]);
                }

                vector<int> logExts(6);

                logExts[0] = blocks[i].minGlobalLogicalExtents[0];
                logExts[1] = blocks[i].minGlobalLogicalExtents[1];
                logExts[2] = blocks[i].minGlobalLogicalExtents[2];

                logExts[3] = blocks[i].maxGlobalLogicalExtents[0]-1;
                if (dimension >= 2)
                    logExts[4] = blocks[i].maxGlobalLogicalExtents[1]-1;
                else
                    logExts[4] = blocks[i].maxGlobalLogicalExtents[1];
                if (dimension >= 3)
                    logExts[5] = blocks[i].maxGlobalLogicalExtents[2]-1;
                else
                    logExts[5] = blocks[i].maxGlobalLogicalExtents[2];

                dn->SetNestingForDomain(FLASHIdToVisitId[i], blocks[i].level-1,
                                        childBlocks, logExts);

                // Instead of finding a representative block for each level, we set the
                // level cell size for each block. Less bookkeeping and the calculation
                // is not that expensive
                vector<double> cs(3);
                cs[0] = 0.0;
                cs[1] = 0.0;
                cs[2] = 0.0;
                for (int d=0 ; d<dimension; ++d)
                {
                    double minExt = blocks[i].minSpatialExtents[d];
                    double maxExt = blocks[i].maxSpatialExtents[d];
                    cs[d] = (maxExt-minExt) / double(block_ndims[d]-1);
                }
                dn->SetLevelCellSizes(blocks[i].level-1, cs);
            }

            void_ref_ptr vr = void_ref_ptr(dn,
                                         avtStructuredDomainNesting::Destruct);

            cache->CacheVoidRef("amr_mesh",
                                AUXILIARY_DATA_DOMAIN_NESTING_INFORMATION,
                                timestep, -1, vr);
            visitTimer->StopTimer(t2, "FLASH setting up patch nesting");
        }

        if (addStructuredDomainBoundaries)
        {
            int t1 = visitTimer->StartTimer();
            avtRectilinearDomainBoundaries *rdb = new avtRectilinearDomainBoundaries(true);
            rdb->SetNumDomains(numBlocks);
            rdb->SetRefinementRatios(refinement_ratios);
            for (i = 0; i < numBlocks; i++)
            {
                int logExts[6];
                logExts[0] = blocks[i].minGlobalLogicalExtents[0];
                logExts[1] = blocks[i].maxGlobalLogicalExtents[0];
                logExts[2] = blocks[i].minGlobalLogicalExtents[1];
                logExts[3] = blocks[i].maxGlobalLogicalExtents[1];
                logExts[4] = blocks[i].minGlobalLogicalExtents[2];
                logExts[5] = blocks[i].maxGlobalLogicalExtents[2];
                rdb->SetIndicesForAMRPatch(FLASHIdToVisitId[i], blocks[i].level - 1, logExts);
            }
            rdb->CalculateBoundaries();

            void_ref_ptr vrdb = void_ref_ptr(rdb,
                                             avtStructuredDomainBoundaries::Destruct);
            cache->CacheVoidRef("any_mesh", AUXILIARY_DATA_DOMAIN_BOUNDARY_INFORMATION,
                                timestep, -1, vrdb);
            visitTimer->StopTimer(t1, "FLASH setting up domain boundaries");
        }
    }

    //  ***********************************************************************
    //  PROCESS THE "mesh_blockandproc" MESH
    //  ***********************************************************************

    if (showProcessors)
    {
        // first, look to see if we don't already have it cached
        void_ref_ptr vrTmp2 = cache->GetVoidRef("mesh_blockandproc",
                                       AUXILIARY_DATA_DOMAIN_NESTING_INFORMATION,
                                       timestep, -1);
    
        if ((*vrTmp2 == NULL))
        {
            int i;
    
            avtRectilinearDomainBoundaries *rdb = new avtRectilinearDomainBoundaries(true);
            rdb->SetNumDomains(numBlocks);
            for (i = 0; i < numBlocks; i++)
            {
                int logExts[6];
                logExts[0] = blocks[i].minGlobalLogicalExtents[0];
                logExts[1] = blocks[i].maxGlobalLogicalExtents[0];
                logExts[2] = blocks[i].minGlobalLogicalExtents[1];
                logExts[3] = blocks[i].maxGlobalLogicalExtents[1];
                logExts[4] = blocks[i].minGlobalLogicalExtents[2];
                logExts[5] = blocks[i].maxGlobalLogicalExtents[2];
                rdb->SetIndicesForAMRPatch(FLASHIdToVisitId[i], blocks[i].level - 1, logExts);
            }
            rdb->CalculateBoundaries();
    
            void_ref_ptr vrdb = void_ref_ptr(rdb,
                                             avtStructuredDomainBoundaries::Destruct);
            cache->CacheVoidRef("any_mesh", AUXILIARY_DATA_DOMAIN_BOUNDARY_INFORMATION,
                                timestep, -1, vrdb);
    
            //
            // build the avtDomainNesting object
            //
    
            if (numLevels > 0)
            {
                avtStructuredDomainNesting *dn =
                    new avtStructuredDomainNesting(numBlocks, numLevels);
    
                dn->SetNumDimensions(dimension);
    
                //
                // Set refinement level ratio information
                //
    
                // NOTE: FLASH files always have a 2:1 ratio
                vector<int> ratios(3);
                ratios[0] = 1;
                ratios[1] = 1;
                ratios[2] = 1;
                dn->SetLevelRefinementRatios(0, ratios);
                for (i = 1; i < numLevels; i++)
                {
                    vector<int> ratios(3);
                    ratios[0] = 2;
                    ratios[1] = 2;
                    ratios[2] = 2;
                    dn->SetLevelRefinementRatios(i, ratios);
                }
    
                //
                // set each domain's level, children and logical extents
                //
                for (i = 0; i < numBlocks; i++)
                {
                    vector<int> childBlocks;
                    for (int j = 0; j < numChildrenPerBlock; j++)
                    {
                        // if this is allowed to be 1-origin, the "-1" here
                        // needs to be removed
                        if (blocks[i].childrenIDs[j] >= 0)
                            childBlocks.push_back(FLASHIdToVisitId[blocks[i].childrenIDs[j] - 1]);
                    }
    
                    vector<int> logExts(6);
    
                    logExts[0] = blocks[i].minGlobalLogicalExtents[0];
                    logExts[1] = blocks[i].minGlobalLogicalExtents[1];
                    logExts[2] = blocks[i].minGlobalLogicalExtents[2];
    
                    logExts[3] = blocks[i].maxGlobalLogicalExtents[0]-1;
                    if (dimension >= 2)
                        logExts[4] = blocks[i].maxGlobalLogicalExtents[1]-1;
                    else
                        logExts[4] = blocks[i].maxGlobalLogicalExtents[1];
                    if (dimension >= 3)
                        logExts[5] = blocks[i].maxGlobalLogicalExtents[2]-1;
                    else
                        logExts[5] = blocks[i].maxGlobalLogicalExtents[2];
    
                    dn->SetNestingForDomain(FLASHIdToVisitId[i], blocks[i].level-1,
                                            childBlocks, logExts);
                }
    
                void_ref_ptr vr = void_ref_ptr(dn,
                                             avtStructuredDomainNesting::Destruct);
    
                cache->CacheVoidRef("mesh_blockandproc",
                                    AUXILIARY_DATA_DOMAIN_NESTING_INFORMATION,
                                    timestep, -1, vr);
            }
        }
    }
}


// ****************************************************************************
//  Method:  avtFLASHFileFormat::GetAuxiliaryData
//
//  Purpose:
//    Right now this only supports spatial interval trees.  There is no
//    other information like materials and species available.
//
//  Arguments:
//    type       the kind of auxiliary data to create
//
//  Programmer:  Jeremy Meredith
//  Creation:    August 23, 2005
//
//  Modifications:
//    Jeremy Meredith, Tue Sep 27 14:32:26 PDT 2005
//    Don't attempt if we don't have any grid data in this file (i.e. only
//    particles in the file).
//
//    Kathleen Bonnell, Mon Aug 14 16:40:30 PDT 2006
//    API change for avtIntervalTree.
//
//    Hank Childs, Tue Dec 15 14:30:07 PST 2009
//    Reorder indices to accommodate reordering of patches for SIL efficiency.
//
// ****************************************************************************
void *
avtFLASHFileFormat::GetAuxiliaryData(const char *var, int dom, 
                                     const char * type, void *,
                                     DestructorFunction &df)
{
    if (type != AUXILIARY_DATA_SPATIAL_EXTENTS)
        return NULL;

    if (numBlocks == 0)
        return NULL;

    avtIntervalTree *itree = new avtIntervalTree(numBlocks, 3);

    for (int b = 0 ; b < numBlocks ; b++)
    {
        double bounds[6];
        bounds[0] = blocks[b].minSpatialExtents[0];
        bounds[1] = blocks[b].maxSpatialExtents[0];
        bounds[2] = blocks[b].minSpatialExtents[1];
        bounds[3] = blocks[b].maxSpatialExtents[1];
        bounds[4] = blocks[b].minSpatialExtents[2];
        bounds[5] = blocks[b].maxSpatialExtents[2];
        itree->AddElement(FLASHIdToVisitId[b], bounds);
    }
    itree->Calculate(true);

    df = avtIntervalTree::Destruct;

    return ((void *) itree);
}


// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadVersionInfo
//
//  Purpose:
//    Read the version info.
//
//  Arguments:
//    none
//
//  Programmer:  Kathleen Bonnell 
//  Creation:    July 18, 2006 
//
//  Modifications:
//    Kathleen Bonnell, Fri Aug 18 16:47:44 PDT 2006
//    Add test for particles files, as version test cannot be done for them
//    in the usual manner.
//
//    Randy Hudson, February 19, 2008
//    Added code to read the "sim info" hdf5 dataset so "file format version"
//    could be read from it, since the latter now has 2 values.
//
//    Randy Hudson, August 8, 2008
//    Added support for particles of file format version 9 by allowing further
//    testing beyond the finding of "particle names"
//
// ****************************************************************************

void
avtFLASHFileFormat::ReadVersionInfo(hid_t file_id)
{
    debug5 << "Determining FLASH file format version." << endl;
    // temporarily disable error reporting
    H5E_auto_t  old_errorfunc;
    void       *old_clientdata;
    H5Eget_auto(&old_errorfunc, &old_clientdata);
    H5Eset_auto(NULL, NULL);

    // If this is a FLASH3 Particles file, or a FLASH3 file with particles, 
    // then it will have the "particle names" field.  If, in addition, it's a
    // file format version (FFV) 9 file, it can have "file format version" and 
    // "sim info", so further checking is needed.  Further checking is also
    // needed for non-particle files.  So...further checking all around.

    int flash3_particles = 0;   //  Init to false
    hid_t h5_PN = H5Dopen(file_id, "particle names");
    if (h5_PN >= 0)
    {
        flash3_particles = 1;
        debug5 << " Found particle names, assuming FLASH3; need to test for file format version 8 or 9" << endl;
        H5Dclose(h5_PN);
    }

    //
    // Read the file format version  (<= 7 means FLASH2)
    //
    hid_t h5_FFV = H5Dopen(file_id, "file format version");

    if (h5_FFV < 0)
    {
        debug5 << "File format version not found in global attributes.  " 
               << "Looking for sim info." << endl;
        hid_t h5_SI = H5Dopen(file_id, "sim info");
        if (h5_SI < 0)
        {
            debug5 << "sim info not found, assuming FLASH2...unless FLASH3 particles" << endl;
            if (flash3_particles == 1)
            {
                fileFormatVersion = FLASH3_FFV8;
            }
            else
            {
                fileFormatVersion = 7;
            }
        }
        else
        {
            debug5 << "sim info found; reading it to get file format version."  << endl;

            //
            // Read the "sim info" components
            //
            hid_t si_type = H5Tcreate(H5T_COMPOUND, sizeof(sim_info_t));
            H5Tinsert(si_type, "file format version", HOFFSET(sim_info_t, file_format_version), H5T_STD_I32LE);
            H5Tinsert(si_type, "setup call",          HOFFSET(sim_info_t, setup_call),          H5T_STRING);
            H5Tinsert(si_type, "file creation time",  HOFFSET(sim_info_t, file_creation_time),  H5T_STRING);
            H5Tinsert(si_type, "flash version",       HOFFSET(sim_info_t, flash_version),       H5T_STRING);
            H5Tinsert(si_type, "build date",          HOFFSET(sim_info_t, build_date),          H5T_STRING);
            H5Tinsert(si_type, "build dir",           HOFFSET(sim_info_t, build_dir),           H5T_STRING);
            H5Tinsert(si_type, "build machine",       HOFFSET(sim_info_t, build_machine),       H5T_STRING);
            H5Tinsert(si_type, "cflags",              HOFFSET(sim_info_t, cflags),              H5T_STRING);
            H5Tinsert(si_type, "fflags",              HOFFSET(sim_info_t, fflags),              H5T_STRING);
            H5Tinsert(si_type, "setup time stamp",    HOFFSET(sim_info_t, setup_time_stamp),    H5T_STRING);
            H5Tinsert(si_type, "build time stamp",    HOFFSET(sim_info_t, build_time_stamp),    H5T_STRING);
    
            H5Dread(h5_SI, si_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, &simInfo);
    
            // Done with the type
            H5Tclose(si_type);
    
            // Done with the variable; don't leak it
            H5Dclose(h5_SI);

            fileFormatVersion = simInfo.file_format_version;
        }
        // turn back on error reporting
        H5Eset_auto(old_errorfunc, old_clientdata);
        return;
    }

    if (flash3_particles == 1)
    {
        fileFormatVersion = FLASH3_FFV8;
    }
    else
    {
        // FLASH 2 has file format version available in global attributes.
        H5Dread(h5_FFV, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, 
                &fileFormatVersion);
    }

    H5Dclose(h5_FFV);
    // turn back on error reporting
    H5Eset_auto(old_errorfunc, old_clientdata);
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadIntegerScalars
//
//  Purpose:
//    Read the integer scalars from the file.
//
//  Arguments:
//    none
//
//  Programmer:  Kathleen Bonnell 
//  Creation:    July 18, 2006 
//
//  Modifications:
//     Randy Hudson, February, 2008
//        Changed test of fileFormatVersion from "!=8" to "<8" to accomodate
//        new value.
//
// ****************************************************************************

void 
avtFLASHFileFormat::ReadIntegerScalars(hid_t file_id)
{
    // Should only be used for FLASH3 files

    if (fileFormatVersion < FLASH3_FFV8)
        return;

    hid_t intScalarsId = H5Dopen(file_id, "integer scalars");
    //
    //
    // Read the integer scalars
    //
    if (intScalarsId < 0)
    {
        debug5 <<  "FLASH3  could not read integer scalars"<< endl;
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t spaceId = H5Dget_space(intScalarsId);
    if (spaceId < 0)
    {
        debug5 << "FLASH3 could not get the space of integer scalars" << endl;
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hsize_t scalarDims[1];
    hsize_t ndims = H5Sget_simple_extent_dims(spaceId, scalarDims, NULL); (void) ndims;
    int nScalars = scalarDims[0];

    hid_t datatype = H5Tcreate(H5T_COMPOUND, sizeof(IntegerScalars));

    hid_t string20 = H5Tcopy(H5T_C_S1);
    H5Tset_size(string20, 20);

    H5Tinsert(datatype, "name", HOFFSET(IntegerScalars,name), string20);
    H5Tinsert(datatype, "value", HOFFSET(IntegerScalars,value), H5T_NATIVE_INT);
    IntegerScalars *is = new IntegerScalars[nScalars];

    H5Dread(intScalarsId, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, is);

    for (int i = 0; i < nScalars; i++)
    { 
        if (strncmp(is[i].name, "nxb", 3) == 0)
            simParams.nxb = is[i].value;
        else if (strncmp(is[i].name, "nyb", 3) == 0)
            simParams.nyb = is[i].value;
        else if (strncmp(is[i].name, "nzb", 3) == 0)
            simParams.nzb = is[i].value;
        else if (strncmp(is[i].name, "globalnumblocks", 15) == 0)
            simParams.total_blocks = is[i].value;
        else if (strncmp(is[i].name, "nstep", 5) == 0)
            simParams.nsteps = is[i].value;
    } 
    // Done with the variable; don't leak it
    H5Tclose(string20);
    H5Tclose(datatype);
    H5Sclose(spaceId);
    H5Dclose(intScalarsId);

    delete [] is;
}

// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadRealScalars
//
//  Purpose:
//    Read the real scalars from the file.
//
//  Arguments:
//    none
//
//  Programmer:  Kathleen Bonnell 
//  Creation:    July 18, 2006 
//
//  Modifications:
//     Randy Hudson, February, 2008
//        Changed test of fileFormatVersion from "!=8" to "<8" to accomodate
//        new value.
//
// ****************************************************************************

void 
avtFLASHFileFormat::ReadRealScalars(hid_t file_id)
{
    // Should only be used for FLASH3 files

    if (fileFormatVersion < FLASH3_FFV8)
        return;

    hid_t realScalarsId = H5Dopen(file_id, "real scalars");
    //
    // Read the real scalars
    //
    if (realScalarsId < 0)
    {
        debug5 << "FLASH3 could not read real scalars" << endl;
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hid_t spaceId = H5Dget_space(realScalarsId);
    if (spaceId < 0)
    {
        debug5 << "FLASH3 could not get the space of real scalars" << endl;
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    hsize_t scalarDims[10];
    hsize_t ndims = H5Sget_simple_extent_dims(spaceId, scalarDims, NULL); (void) ndims;

    int nScalars = scalarDims[0];

    hid_t datatype = H5Tcreate(H5T_COMPOUND, sizeof(RealScalars));

    hid_t string20 = H5Tcopy(H5T_C_S1);
    H5Tset_size(string20, 20);

    H5Tinsert(datatype, "name", HOFFSET(RealScalars,name), string20);
    H5Tinsert(datatype, "value", HOFFSET(RealScalars,value), H5T_NATIVE_DOUBLE);

    RealScalars *rs = new RealScalars[nScalars];

    H5Dread(realScalarsId, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, rs);

    for (int i = 0; i < nScalars; i++)
    { 
        if (strncmp(rs[i].name, "time", 4) == 0)
            simParams.time = rs[i].value;
    } 
    // Done with the variable; don't leak it
    H5Tclose(string20);
    H5Tclose(datatype);
    H5Sclose(spaceId);
    H5Dclose(realScalarsId);
    delete [] rs;
}


// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadParticleAttributes_FLASH3
//
//  Purpose:
//    Read the the variable names and the dims for the particle attributes.
//
//  Arguments:
//    none
//
//  Programmer:  Kathleen Bonnell 
//  Creation:    July 18, 2006 
//
//  Modifications:
//     Randy Hudson, February, 2008
//        Changed test of fileFormatVersion from "!=8" to "<8" to accomodate
//        new value.
//
// ****************************************************************************

void
avtFLASHFileFormat::ReadParticleAttributes_FLASH3()
{
    // Should only be used for FLASH3 files

    if (fileFormatVersion < FLASH3_FFV8)
        return;

    // temporarily disable error reporting
    H5E_auto_t  old_errorfunc;
    void       *old_clientdata;
    H5Eget_auto(&old_errorfunc, &old_clientdata);
    H5Eset_auto(NULL, NULL);

    hid_t pnameId = H5Dopen(fileId, "particle names");

    // turn back on error reporting
    H5Eset_auto(old_errorfunc, old_clientdata);

    // do we have particle names?
    if (pnameId < 0)
    {
        debug5 << "FLASH3 no particles names" << endl;
        numParticles = 0; 
        return;
    }
    
    hid_t pnamespace = H5Dget_space(pnameId);
    hsize_t dims[10];
    hsize_t ndims =  H5Sget_simple_extent_dims(pnamespace, dims, NULL);

    // particle names ndims should be 2, and if the second dim isn't 1,
    // need to come up with a way to handle it!
    if (ndims != 2 || dims[1] != 1) 
    {
        if (ndims != 2)
        {
            debug5 << "FLASH3 expecting particle names ndims of 2, got "  
                   << ndims << endl;
        }
        if (dims[1] != 1)
        {
            debug5 << "FLASH3 expecting particle names dims[1] of 1, got "  
                   << dims[1] << endl;
        }
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }

    int numNames = dims[0];

    // create the right-size string, and a char array to read the data into
    hid_t string24 = H5Tcopy(H5T_C_S1);
    H5Tset_size(string24, 24);
    char *cnames = new char[24*numNames];
    H5Dread(pnameId, string24, H5S_ALL, H5S_ALL, H5P_DEFAULT, cnames);

    // Convert the single string to individual variable names.
    string  snames(cnames);
    delete[] cnames;
    for (int i = 0; i < numNames; i++)
    { 
        string name = snames.substr(i*24, 24);
        int sp = name.find_first_of(' ');
        if (sp < 24)
            name = name.substr(0, sp);
        string nice_name = GetNiceParticleName(name);
        particleVarTypes.push_back(H5T_NATIVE_DOUBLE);
        particleVarNames.push_back(name);
        particleOriginalIndexMap[nice_name] = i;

        // We read the particles before the grids.  Just in case we
        // don't have any grids, take a stab at the problem dimension
        // based purely on the existence of various data members.
        // This will be overwritten by the true grid topological
        // dimension if the grid exists.
        if (name == "posx" && dimension < 1)
            dimension = 1;
        if (name == "posy" && dimension < 2)
            dimension = 2;
        if (name == "posz" && dimension < 3)
            dimension = 3;
    } 
    H5Tclose(string24);
    H5Sclose(pnamespace);
    H5Dclose(pnameId);
   
    // 
    // Read particle dimensions and particle HDFVarName 
    // 

    // temporarily disable error reporting
    H5Eget_auto(&old_errorfunc, &old_clientdata);
    H5Eset_auto(NULL, NULL);

    // find the particle variable (if it exists)
    hid_t pointId;
    particleHDFVarName = "particle tracers";
    pointId = H5Dopen(fileId, particleHDFVarName.c_str());
    if (pointId < 0)
    {
        particleHDFVarName = "tracer particles";
        pointId = H5Dopen(fileId, particleHDFVarName.c_str());
    }

    // turn back on error reporting
    H5Eset_auto(old_errorfunc, old_clientdata);

    // Doesn't exist?  No problem -- we just don't have any particles
    if (pointId < 0)
    {
        debug5 << "FLASH3 no tracer particles" << endl;
        numParticles = 0;
        return;
    }

    hid_t pointSpaceId = H5Dget_space(pointId);

    hsize_t p_dims[10];
    hsize_t p_ndims =  H5Sget_simple_extent_dims(pointSpaceId, p_dims, NULL);
    if (p_ndims != 2)
    {
        debug5 << "FLASH3, expecting particle tracer ndims of 2, got"
               << p_ndims << endl;
        EXCEPTION1(InvalidFilesException, filename.c_str());
    }
    numParticles = p_dims[0];

    H5Sclose(pointSpaceId);
    H5Dclose(pointId);
} 



// ****************************************************************************
//  Method:  avtFLASHFileFormat::ReadParticleVar
//
//  Purpose:
//    Read the data associated with a particle var.
//
//  Arguments:
//    pointId    The identifier for the particles dataset.
//    vname      The name of the variable to retrieve
//    ddata      A place to store the data. 
//
//  Notes:
//    Assumes the particles dataset associated with pointId is already opened
//    and will be closed by calling method.
//    Assumes ddata has already been created to appropriate size.
//
//  Programmer:  Kathleen Bonnell 
//  Creation:    July 18, 2006 
//
//  Modifications:
//
//    Hank Childs, Thu Mar  8 10:00:33 PST 2007
//    Use version macro to get around hsize_t/hssize_t problem.
//
//     Randy Hudson, February, 2008
//        Changed test of fileFormatVersion from "!=8" to "<8" to accomodate
//        new value.
//
// ****************************************************************************

void
avtFLASHFileFormat::ReadParticleVar(hid_t pointId, const char *vname, 
    double *ddata)
{
    // Should only be used for FLASH3 files

    if (fileFormatVersion < FLASH3_FFV8)
        return;

    hsize_t np = static_cast<hsize_t>(numParticles);
    hsize_t dataspace = H5Dget_space(pointId);
    hsize_t memdims[1] = {np};
    hsize_t memspace = H5Screate_simple(1, memdims, NULL);
    int index = particleOriginalIndexMap[vname];

#if HDF5_VERSION_GE(1,6,4)
    hsize_t offset[2];
#else
    hssize_t offset[2];
#endif
    offset[0] = 0;
    offset[1] = index;
    hsize_t count[2] = {np, 1}; 

    H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, 
                                    count, NULL);
    H5Dread(pointId, H5T_NATIVE_DOUBLE, memspace, dataspace, 
                        H5P_DEFAULT, ddata); 
 
    H5Sclose(dataspace);
    H5Sclose(memspace);
}
