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/*****************************************************************************
*
* Copyright (c) 2000 - 2010, Lawrence Livermore National Security, LLC
* Produced at the Lawrence Livermore National Laboratory
* LLNL-CODE-400124
* All rights reserved.
*
* This file is part of VisIt. For details, see https://visit.llnl.gov/. The
* full copyright notice is contained in the file COPYRIGHT located at the root
* of the VisIt distribution or at http://www.llnl.gov/visit/copyright.html.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* - Redistributions of source code must retain the above copyright notice,
* this list of conditions and the disclaimer below.
* - Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the disclaimer (as noted below) in the
* documentation and/or other materials provided with the distribution.
* - Neither the name of the LLNS/LLNL nor the names of its contributors may
* be used to endorse or promote products derived from this software without
* specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY,
* LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
* DAMAGE.
*
*****************************************************************************/
// ************************************************************************* //
// avtSAMRAIFileFormat.h //
// ************************************************************************* //
#ifndef AVT_SAMRAI_FILE_FORMAT_H
#define AVT_SAMRAI_FILE_FORMAT_H
#include <avtSTMDFileFormat.h>
#include <vector>
#include <string>
#include <map>
#include <visitstream.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 <hdf5.h>
using std::string;
using std::vector;
using std::map;
class avtMaterial;
class avtSpecies;
// ****************************************************************************
// Class: avtSAMRAIFileFormat
//
// Purpose:
// A file format reader for single-timestep, multi-domain SAMRAI files.
//
// Programmer: Walter Herrera-Jimenez
// Creation: July 7, 2003
//
// Modifications:
//
// Mark C. Miller, Mon Dec 8 13:54:21 PST 2003
// Added constants for expected version number, and enviornment variable
// used to disable version checking. Added var_num_ghosts array. Added
// prototype for RegisterVariableList
//
// Kathleen Bonnell, Fri Dec 19 10:20:57 PST 2003
// Moved 'expected_version_number' to source file so that code will build
// on IRIX.
//
// Mark C. Miller, Thu Jan 29 11:21:41 PST 2004
// Added var_max_ghost data member
//
// Mark C. Miller, Mon Aug 23 14:17:55 PDT 2004
// Added methods PopulateIOInformation, OpenFile, CloseFile and data
// member h5files
//
// Mark C. Miller, Thu Nov 18 18:04:01 PST 2004
// Added FreeUpResources
//
// Hank Childs, Sat Mar 5 10:35:11 PST 2005
// Added ActivateTimestep.
//
// Mark C. Miller, Tue Nov 8 20:56:46 PST 2005
// Moved implementation of GetCycle to .C file. Added GetTime and
// GetCycleFromFilename
//
// Mark C. Miller, Mon Nov 5 19:34:12 PST 2007
// Added support for sparse material representation and expressions
//
// ****************************************************************************
class avtSAMRAIFileFormat : public avtSTMDFileFormat
{
public:
avtSAMRAIFileFormat(const char *);
~avtSAMRAIFileFormat();
bool HasInvariantMetaData(void) const { return false; };
bool HasInvariantSIL(void) const { return false; };
bool CanCacheVariable(const char *);
virtual const char *GetType(void) { return "SAMRAI File Format"; };
vtkDataSet *GetMesh(int, const char *);
vtkDataArray *GetVar(int, const char *);
vtkDataArray *GetVectorVar(int, const char *);
avtMaterial *GetMaterial(int, const char *);
avtSpecies *GetSpecies(int, const char *);
void *GetAuxiliaryData(const char *var, int,
const char *type, void *args,
DestructorFunction &);
int GetCycleFromFilename(const char *f) const;
int GetCycle(void);
double GetTime(void);
void PopulateDatabaseMetaData(avtDatabaseMetaData *);
void PopulateIOInformation(avtIOInformation &ioInfo);
void RegisterVariableList(const char *,
const vector<CharStrRef> &);
hid_t OpenFile(const char *fileName);
void CloseFile(int f);
void FreeUpResources(void);
void ActivateTimestep(void);
protected:
typedef struct {
int processor_number;
int file_cluster_number;
int level_number;
int patch_number;
} patch_map_t;
typedef struct {
int lower[3];
int upper[3];
double xlo[3];
double xup[3];
} patch_extents_t;
typedef struct {
char data_is_defined;
double min;
double max;
} var_extents_t;
typedef struct {
int num_components;
int cell_centered;
int num_ghosts[3];
} var_t;
typedef struct {
int offset;
int number_children;
} child_t;
typedef struct {
int offset;
int number_parents;
} parent_t;
typedef struct {
unsigned char data_is_defined;
int mat_comp_flag;
int spec_comp_flag;
double min;
double max;
} matinfo_t;
vtkDataSet ***cached_patches;
string file_name;
string dir_name;
bool have_read_metadata_file;
string grid_type;
int time_step_number;
double time;
string time_dump;
double *xlo;
double *dx;
int num_dim_problem;
int num_levels;
int num_patches;
int *num_patches_level;
int *ratios_coarser_levels;
int num_clusters;
int num_procs;
int num_vars;
int *var_cell_centered;
int *var_num_components;
int *var_num_ghosts;
int var_max_ghosts[3];
string *var_names;
map<string, var_t> var_names_num_components;
bool has_mats;
bool inferVoidMaterial;
int num_mats;
string *mat_names;
int *mat_num_ghosts;
int num_mat_vars;
int *mat_var_num_components;
string *mat_var_names;
map<string, var_t> mat_var_names_num_components;
map<string, matinfo_t*> mat_names_matinfo;
map<string, map<string, matinfo_t*> > mat_var_names_matinfo;
matinfo_t *sparse_mat_info;
bool has_specs;
int num_spec_vars;
string *spec_var_names;
int *nmatspec;
map<string, string*> mat_specs;
map<string, map<string, matinfo_t*> > mat_specs_matinfo;
var_extents_t **var_extents;
patch_extents_t *patch_extents;
patch_map_t *patch_map;
int *child_array;
int child_array_length;
child_t *child_pointer_array;
int *parent_array;
int parent_array_length;
parent_t *parent_pointer_array;
bool has_ghost;
bool ghosting_is_consistent;
string active_visit_var_name;
string last_visit_var_name;
int last_patch;
int num_exprs;
string *expr_keys;
string *expr_types;
string *expr_defns;
hid_t *h5files;
static int objcnt;
static void InitializeHDF5();
static void FinalizeHDF5();
virtual vtkDataSet *ReadMesh(int);
vtkDataArray *ReadVar(int patch, const char *visit_var_name);
void ReadAndCheckVDRVersion(hid_t &h5_file);
void ReadGridType(hid_t &h5_file);
void ReadTime(hid_t &h5_file);
void ReadTimeStepNumber(hid_t &h5_file);
void ReadTimeOfDump(hid_t &h5_file);
void ReadNumDimensions(hid_t &h5_file);
void ReadXLO(hid_t &h5_file);
void ReadDX(hid_t &h5_file);
void ReadNumLevels(hid_t &h5_file);
void ReadNumPatches(hid_t &h5_file);
void ReadNumPatchesLevel(hid_t &h5_file);
void ReadRatiosCoarserLevels(hid_t &h5_file);
void ReadNumClusters(hid_t &h5_file);
void ReadNumProcessors(hid_t &h5_file);
void ReadNumVariables(hid_t &h5_file);
void ReadVarCellCentered(hid_t &h5_file);
void ReadVarNames(hid_t &h5_file);
void ReadVarNumComponents(hid_t &h5_file);
void ReadVarNumGhosts(hid_t &h5_file);
void ReadVarExtents(hid_t &h5_file);
void ReadPatchExtents(hid_t &h5_file);
void ReadPatchMap(hid_t &h5_file);
void ReadChildArrayLength(hid_t &h5_file);
void ReadChildArray(hid_t &h5_file);
void ReadChildPointerArray(hid_t &h5_file);
void ReadParentArrayLength(hid_t &h5_file);
void ReadParentArray(hid_t &h5_file);
void ReadParentPointerArray(hid_t &h5_file);
void ReadExpressions(hid_t &h5_file);
void ReadMaterialInfo(hid_t &h5_file);
avtMaterial *ReadSparseMaterialData(int patch, const int *matnos,
const char **matnames);
float *ReadMatSpecFractions(int, string, string="");
void ConvertVolumeFractionFields(vector<int> matIds, float **vfracs,
int ncells, int* &matfield, int &mixlen, int* &mix_mat,
int* &mix_next, int* &mix_zone, float* &mix_vf);
char DebugMixedMaterials(int ncells, int* &matfield, int* &mix_next,
int* &mix_mat, float* &mix_vf, int* &mix_zone);
void ReadSpeciesInfo(hid_t &h5_file);
void ConvertMassFractionFields(vector<int> matIds,
vector<float**> sfracs, int ncells, avtMaterial *mat,
int* &speclist, int &nspecies_mf, float* &species_mf,
int* &mixList);
void BuildDomainAuxiliaryInfo();
void ReadMetaDataFile();
int GetGhostCodeForVar(const char * visit_var_name);
bool ReadDataset(hid_t &h5_file, const char *dspath, const char *typeName,
int ndims, int *dims, void **data, bool isOptional=true);
};
#define DEFAULT_SIZE 1024
#define DEFAULT_MINC 2.0
class UniqueSpeciesMF
{
public:
UniqueSpeciesMF(int initSize = DEFAULT_SIZE, float _minc = DEFAULT_MINC);
~UniqueSpeciesMF();
int IndexOfMFVector(float *mf_vector, int nvals);
float *GetData();
int GetSize();
int GetMaxSize();
private:
static int DefaultSize;
static float DefaultMinc;
// this is solely to control default construction of mapped values
struct Index {
int idx;
Index() : idx(-1) {}
};
map<unsigned int,Index> vmap;
bool dataRetrieved;
float minc;
int max_nspecies_mf;
int nspecies_mf;
float *species_mf;
};
#endif
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