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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.
*
*****************************************************************************/
// ************************************************************************* //
// avtSiloFileFormat.h //
// ************************************************************************* //
#ifndef AVT_SILO_FILE_FORMAT_H
#define AVT_SILO_FILE_FORMAT_H
#include <avtDataSelection.h>
#include <avtSTMDFileFormat.h>
#include <string>
#include <vector>
#include <map>
#include <set>
#include <silo.h>
#include <void_ref_ptr.h>
using std::string;
using std::vector;
using std::map;
class vtkUnstructuredGrid;
class avtFacelist;
class avtIntervalTree;
class avtMaterial;
class avtSpecies;
class DBOptionsAttributes;
typedef struct _GroupInfo
{
_GroupInfo() : haveGroups(false), ndomains(0), numgroups(0) {}
bool haveGroups;
int ndomains;
int numgroups;
vector<int> ids;
} GroupInfo;
// ****************************************************************************
// Class: avtSiloFileFormat
//
// Purpose:
// A Silo file format reader.
//
// Programmer: Hank Childs
// Creation: February 23, 2001
//
// Modifications:
//
// Hank Childs, Tue Mar 20 09:53:40 PST 2001
// Allowed for reading vector variables.
//
// Hank Childs, Fri May 11 11:35:16 PDT 2001
// Added I/O hints to tune performance.
//
// Kathleen Bonnell, Tue Jun 12 13:23:24 PDT 2001
// Add method to get ghost zones from quad meshes.
//
// Hank Childs, Fri Nov 2 14:41:59 PST 2001
// Read in variables from directories beyond the top level.
//
// Eric Brugger, Fri Dec 7 13:39:42 PST 2001
// I modified CloseFile to be virtual.
//
// Jeremy Meredith, Thu Dec 13 17:52:43 PST 2001
// Added species support.
//
// Kathleen Bonnell, Fri Feb 8 11:03:49 PST 2002
// vtkScalars and vtkVectors have been deprecated in VTK 4.0,
// use vtkDataArray instead.
//
// Jeremy Meredith, Wed Mar 19 11:51:39 PST 2003
// Changed DetermineMultiMeshForSubVariable to handle more advanced
// matching. Added some more data members to this effect.
//
// Jeremy Meredith, Tue Jul 15 09:23:45 PDT 2003
// Split out some of ReadDir into its own functions so that parallelizing
// the file reading was easier.
//
// Hank Childs, Thu Aug 14 09:15:55 PDT 2003
// Remove vector defvars support (it is now handled correctly).
//
// Mark C. Miller, Mon Feb 9 16:10:16 PST 2004
// Added interface method, ActivateTimestep
//
// Hank Childs, Fri Feb 13 17:18:04 PST 2004
// Added argument to CalcMaterial.
//
// Mark C. Miller, Mon Feb 23 12:02:24 PST 2004
// Added GetFile() method
// Added optional bools to skip global information during OpenFile
//
// Mark C. Miller, Mon Aug 9 19:12:24 PDT 2004
// Added methods to get global node and zone ids
// Added method to allocate and determine meshame for a ucd mesh
//
// Mark C. Miller, Thu Oct 14 15:18:31 PDT 2004
// Added GetSpatialExtents and GetDataExtents
//
// Mark C. Miller, Thu Oct 21 22:11:28 PDT 2004
// Added arbMeshZoneRangesToSkip to support DBzonelists with arb. zones.
//
// Kathleen Bonnell, Tue Feb 8 13:41:05 PST 2005
// Added int arg to GetQuadMesh.
//
// Mark C. Miller, Tue May 17 18:48:38 PDT 2005
// Added methods to GetCycle/Time
//
// Mark C. Miller, Wed Aug 10 12:00:00 PDT 2005
// Added resample data selections to support CSG mesh discretization
//
// Jeremy Meredith, Tue Sep 13 15:57:05 PDT 2005
// Changed domainDirs to a set to ensure log(n) search times.
//
// Mark C. Miller, Thu Sep 15 11:30:18 PDT 2005
// Added CanCacheVariable, primarily to support csg discretization.
// It will be removed after 3d, adaptive csg discretization is available
// in avtGenericDatabase
//
// Mark C. Miller, Wed Nov 16 10:46:36 PST 2005
// Removed CanCacheVariable
//
// Mark C. Miller, Wed Nov 29 15:08:21 PST 2006
// Added connectivityIsTimeVarying
//
// Mark C. Miller, Sun Dec 3 12:20:11 PST 2006
// Removed RegisterDataSelections. Was only used by CSG stuff
// Added dontForceSingle. Added support for CSG multimeshes and CSG vars
//
// Mark C. Miller, Wed Dec 13 16:55:30 PST 2006
// Added method/data member for explicit multivar to multimesh mapping to
// support time-invariant multimeshes stored in separate files from vars.
//
// Mark C. Miller, Mon Jul 9 14:23:22 PDT 2007
// Added data member codeNameGuess which is to store a guess of the name
// of the code that produced the data.
//
// Mark C. Miller, Tue Aug 28 19:17:44 PDT 2007
// Made it deal with case where multimesh and blocks are all in same
// dir in the file. Added args to DetermineFile[name]AndDirectory to
// support this.
//
// Cyrus Harrison, Fri Sep 7 15:24:27 PDT 2007
// Added FindMultiMeshAdjConnectivity to support the Silo MultiMesh
// Adjacency object.
//
// Hank Childs, Mon Oct 8 13:01:31 PDT 2007
// Added optional argument to GetConnectivityAndGroupInformation.
//
// Mark C. Miller, Wed Feb 6 12:27:09 PST 2008
// Added topDir data member for case where entire time series is in
// a single silo file.
//
// Mark C. Miller, Mon Apr 14 15:41:21 PDT 2008
// Added 'using' statements (above) and removed all 'std::' where
// appropriate. Added GetNodelistVars, AddNodelistEnumerations
//
// Mark C. Miller, Tue Jun 10 22:36:25 PDT 2008
// Added bools to control ignoring of extents.
//
// Jeremy Meredith, Thu Aug 7 16:16:00 EDT 2008
// Made GetComponent accept const char*'s as input.
//
// Cyrus Harrison, Mon Oct 27 10:33:39 PDT 2008
// Added FindDecomposedMeshType() to help with creating the correct type of
// domain boundries object in GetConnectivityAndGroupInformation.
//
// Mark C. Miller, Tue Dec 23 22:14:30 PST 2008
// Added support for ANNOTATION_INT nodelists (special case)
//
// Mark C. Miller, Wed Mar 4 08:54:57 PST 2009
// Added tri-state variables to better manage ignoring of extents.
//
// Mark C. Miller, Mon Mar 16 23:33:32 PDT 2009
// Removed usingOldExtents. Moved logic for 'old' extents interface to
// CommonPluginInfo where old (obsolete) options can be merged with current
// interface.
//
// Mark C. Miller, Thu Jun 18 20:54:17 PDT 2009
// Replaced DBtoc* arg to ReadXXX functions with list of names of objects
// to process. Added RemoveMultixxx functions to help manage cached
// multi-objects in presence of exceptions.
//
// Mark C. Miller, Mon Mar 16 23:33:32 PDT 2009
// Removed usingOldExtents. Moved logic for 'old' extents interface to
// CommonPluginInfo where old (obsolete) options can be merged with current
// interface.
//
// Mark C. Miller, Thu Jun 18 20:54:17 PDT 2009
// Replaced DBtoc* arg to ReadXXX functions with list of names of objects
// to process. Added RemoveMultixxx functions to help manage cached
// multi-objects in presence of exceptions.
//
// Mark C. Miller, Thu Oct 29 15:15:37 PDT 2009
// Removed arbMeshZoneRangesToSkip. Added HandleGlobalZoneIds. Adjusted
// interface to ReadInConnectivity.
//
// Mark C. Miller, Tue Dec 15 13:50:40 PST 2009
// Added HasInvariantMetadata/SIL and metadataIsTimeVarying.
//
// Mark C. Miller, Tue Jan 12 17:48:39 PST 2010
// Made HandleGlobalZoneIds work for different versions of Silo.
//
// Mark C. Miller, Wed Jan 27 13:13:20 PST 2010
// Added an extra level of indirection to the arbMeshXXXRemap maps to
// make sure they work for multi-block case.
//
// Cyrus Harrison, Wed Mar 24 10:59:17 PDT 2010
// Added haveAmrGroupInfo, which is used to prevent collsion of amr
// levels info with connectivity group info.
//
// ****************************************************************************
class avtSiloFileFormat : public avtSTMDFileFormat
{
public:
avtSiloFileFormat(const char *, DBOptionsAttributes*);
virtual ~avtSiloFileFormat();
virtual void FreeUpResources(void);
virtual const char *GetType(void) { return "Silo File Format"; };
virtual void *GetAuxiliaryData(const char *var, int,
const char *type, void *args,
DestructorFunction &);
virtual vtkDataSet *GetMesh(int, const char *);
virtual vtkDataArray *GetVar(int, const char *);
virtual vtkDataArray *GetVectorVar(int, const char *);
avtMaterial *GetMaterial(int, const char *);
avtSpecies *GetSpecies(int, const char *);
avtFacelist *GetExternalFacelist(int, const char *);
virtual void PopulateDatabaseMetaData(avtDatabaseMetaData *);
virtual void PopulateIOInformation(avtIOInformation &);
int GetCycle();
int GetCycleFromFilename(const char *f) const;
double GetTime();
void ActivateTimestep(void);
bool HasInvariantMetaData(void) const { return !metadataIsTimeVarying; };
bool HasInvariantSIL(void) const { return !metadataIsTimeVarying; };
protected:
enum AANTriState {Always=0, Auto, Never};
DBfile **dbfiles;
int tocIndex;
int dontForceSingle; // used primarily for testing
AANTriState ignoreSpatialExtentsAAN;
AANTriState ignoreDataExtentsAAN;
bool ignoreSpatialExtents;
bool ignoreDataExtents;
bool searchForAnnotInt;
bool readGlobalInfo;
bool connectivityIsTimeVarying;
bool metadataIsTimeVarying;
bool hasDisjointElements;
string codeNameGuess;
std::set<string> domainDirs;
// The following fields are for determining multimeshes for multivars
vector<string> firstSubMesh;
vector<string> firstSubMeshVarName;
vector<vector<string> > allSubMeshDirs;
vector<string> actualMeshName;
vector<int> blocksForMesh;
map<string,vector<int> > blocksForMultivar;
vector<DBmultimesh *> multimeshes;
vector<string> multimesh_name;
vector<DBmultivar *> multivars;
vector<string> multivar_name;
vector<DBmultimat *> multimats;
vector<string> multimat_name;
vector<DBmultimatspecies *> multimatspecies;
vector<string> multimatspec_name;
map<string, string> multivarToMultimeshMap;
GroupInfo groupInfo;
bool haveAmrGroupInfo;
map<string, map<int, vector<int>* > > arbMeshCellReMap;
map<string, map<int, vector<int>* > > arbMeshNodeReMap;
vector<avtDataSelection_p> selList;
vector<bool> *selsApplied;
string topDir;
// to support block structured nodelist convention
map<int, vector<int> > nlBlockToWindowsMap;
vector<vector<int> > pascalsTriangleMap;
int numNodeLists;
int maxAnnotIntLists;
DBfile *GetFile(int);
DBfile *OpenFile(int, bool skipGlobalInfo = false);
DBfile *OpenFile(const char *, bool skipGlobalInfo = false);
virtual void CloseFile(int);
void ReadDir(DBfile*,const char*,avtDatabaseMetaData*);
void ReadTopDirStuff(DBfile*,const char*,avtDatabaseMetaData*,char**);
void ReadMultimeshes(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadQuadmeshes(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadUcdmeshes(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadPointmeshes(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadCurves(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadCSGmeshes(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadMultivars(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadQuadvars(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadUcdvars(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadPointvars(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadCSGvars(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadMaterials(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadMultimats(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadSpecies(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadMultispecies(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void ReadDefvars(DBfile*,int,char**,const char*,avtDatabaseMetaData*);
void DoRootDirectoryWork(avtDatabaseMetaData*);
void BroadcastGlobalInfo(avtDatabaseMetaData*);
void StoreMultimeshInfo(const char *const dirname,
const char *const name_w_dir,
int meshnum, const DBmultimesh *const mm);
void AddCSGMultimesh(const char *const dirname,
const char *const multimesh_name,
avtDatabaseMetaData *md,
const DBmultimesh *const mm, DBfile *dbfile);
vtkDataArray *GetNodelistsVar(int);
vtkDataArray *GetAnnotIntNodelistsVar(int, string);
vtkDataArray *GetQuadVar(DBfile *, const char *, const char *,int);
vtkDataArray *GetUcdVar(DBfile *, const char *, const char *, int);
vtkDataArray *GetPointVar(DBfile *, const char *);
vtkDataArray *GetCsgVar(DBfile *, const char *);
vtkDataArray *GetStandardVectorVar(int, const char *);
vtkDataArray *GetQuadVectorVar(DBfile*, const char *, const char *,
int);
vtkDataArray *GetUcdVectorVar(DBfile*,const char*,const char*,int);
vtkDataArray *GetPointVectorVar(DBfile *, const char *);
vtkDataArray *GetCsgVectorVar(DBfile *, const char *);
vtkDataSet *CreateCurvilinearMesh(DBquadmesh *);
vtkDataSet *CreateRectilinearMesh(DBquadmesh *);
vtkDataSet *GetCSGMesh(DBfile *, const char *, int);
vtkDataSet *GetPointMesh(DBfile *, const char *);
vtkDataSet *GetQuadMesh(DBfile *, const char *, int);
vtkDataSet *GetCurve(DBfile *, const char *);
vtkDataSet *GetUnstructuredMesh(DBfile *, const char *,
int, const char *);
#ifdef SILO_VERSION_GE
#if SILO_VERSION_GE(4,7,1)
void HandleGlobalZoneIds(const char *, int, void*, int, int);
#else
void HandleGlobalZoneIds(const char *, int, int*, int);
#endif
#else
void HandleGlobalZoneIds(const char *, int, int*, int);
#endif
void ReadInConnectivity(vtkUnstructuredGrid *,
DBzonelist *, int,
const char *,int);
void ReadInArbConnectivity(const char *, vtkUnstructuredGrid*,
DBucdmesh*,int);
avtMeshType FindDecomposedMeshType(DBfile *dbfile);
void GetConnectivityAndGroupInformation(DBfile *, bool = false);
void GetConnectivityAndGroupInformationFromFile(DBfile *,
int &, int *&,int *&,int &,int *&,int &,int *&);
void FindStandardConnectivity(DBfile *, int &, int *&,
int *&, int &, int *&, int &, int *&, bool, bool);
void FindGmapConnectivity(DBfile *, int &, int *&, int *&,
int &, int *&, int &, int *&, bool, bool);
void FindMultiMeshAdjConnectivity(DBfile *, int &, int *&,
int *&, int &, int *&, int &, int *&,
bool, bool);
void GetMultivarToMultimeshMap(DBfile *);
avtFacelist *CalcExternalFacelist(DBfile *, char *);
avtMaterial *CalcMaterial(DBfile *, char *, const char *, int dom);
avtSpecies *CalcSpecies(DBfile *, char *);
vtkDataArray *GetGlobalNodeIds(int, const char *);
vtkDataArray *GetGlobalZoneIds(int, const char *);
avtIntervalTree *GetSpatialExtents(const char *);
avtIntervalTree *GetDataExtents(const char *);
void GetQuadGhostZones(DBquadmesh *, vtkDataSet *);
void VerifyQuadmesh(DBquadmesh *, const char *);
void DetermineFileAndDirectory(char *, DBfile *&, const char *, char *&,
bool *alloc=0);
void DetermineFilenameAndDirectory(char *, const char *,
char *, char *&, bool *alloc=0);
void GetRelativeVarName(const char *,const char *,char *);
char *AllocAndDetermineMeshnameForUcdmesh(int, const char *);
string DetermineMultiMeshForSubVariable(DBfile*,const char*,
char**,int, const char*);
int GetMeshtype(DBfile *, char *);
void GetMeshname(DBfile *, char *, char *);
void *GetComponent(DBfile *, char *, const char *);
void GetTimeVaryingInformation(DBfile *,
avtDatabaseMetaData *md = NULL);
void GetVectorDefvars(const char *);
void RegisterDomainDirs(const char * const *, int,
const char*);
bool ShouldGoToDir(const char *);
void ReadGlobalInformation(DBfile *);
void AddNodelistEnumerations(DBfile *dbfile, avtDatabaseMetaData *md,
string meshname);
void GetMeshHelper(int *domain, const char *m, DBmultimesh **mm, int *type,
DBfile **_domain_file, char **_directory_mesh,
bool *_allocated_directory_mesh);
void AddAnnotIntNodelistEnumerations(DBfile *dbfile, avtDatabaseMetaData *md,
string meshname, DBmultimesh *mm);
DBmultimesh *GetMultimesh(const char *path, const char *name);
DBmultimesh *QueryMultimesh(const char *path, const char *name);
void RemoveMultimesh(DBmultimesh *mm);
DBmultivar *GetMultivar(const char *path, const char *name);
DBmultivar *QueryMultivar(const char *path, const char *name);
void RemoveMultivar(DBmultivar *mv);
DBmultimat *GetMultimat(const char *path, const char *name);
DBmultimat *QueryMultimat(const char *path, const char *name);
void RemoveMultimat(DBmultimat *mm);
DBmultimatspecies *GetMultimatspec(const char *path, const char *name);
DBmultimatspecies *QueryMultimatspec(const char *path, const char *name);
void RemoveMultimatspec(DBmultimatspecies *ms);
};
#endif
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