1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
|
/*****************************************************************************
*
* 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.
*
*****************************************************************************/
// ************************************************************************* //
// avtFLASHFileFormat.h //
// ************************************************************************* //
#ifndef AVT_FLASH_FILE_FORMAT_H
#define AVT_FLASH_FILE_FORMAT_H
#include <avtSTMDFileFormat.h>
#include <map>
#include <string>
#include <vector>
// 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>
#include <vtkPolyData.h>
class DBOptionsAttributes;
// ****************************************************************************
// Class: avtFLASHFileFormat
//
// Purpose:
// Reads in FLASH files as a plugin to VisIt.
//
// 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 14:22:29 PDT 2005
// Added "new" style particle support.
//
// Hank Childs, Fri Apr 28 14:20:35 PDT 2006
// Added activate timestep.
//
// Kathleen Bonnell, Thu Jul 20 11:22:13 PDT 2006
// Added methods and structs to support for FLASH3 formats.
//
// Mark C. Miller, Mon Mar 5 22:04:50 PST 2007
// Added support for Cycles/Times. Added methods to explicitly initialize
// and finalize the hdf5 library
//
// Mark C. Miller, Tue Mar 6 23:41:33 PST 2007
// Removed simParamsHaveBeenRead; Added bool to ReadSimulationParameters
//
// Randy HUDSON, Tue, Apr 3, 2007
// Added support for Morton curve
//
// Randy HUDSON, Mon, June 18, 2007
// Added support for creating subsets of Morton curve.
//
// Randy HUDSON, July, 2007
// Added support for subsets by processor number.
//
// Randy Hudson, August, 2007
// Added support for concurrent subsets by block-level and block-processornumber
// pairs for both the domain and Morton curve.
//
// Randy Hudson, February, 2008
// Added struct for "sim info" HDF5 DATASET so "file format version" can be read
//
// Hank Childs, Fri Dec 11 13:15:13 PST 2009
// Add support for the new, more efficient way of handling AMR meshes in the
// SIL.
//
// Hank Childs, Thu Dec 17 14:07:52 PST 2009
// Add support for database options.
//
// Hank Childs, Sat Mar 20 20:21:47 PDT 2010
// Add data members for more database options.
//
// ****************************************************************************
class avtFLASHFileFormat : public avtSTMDFileFormat
{
public:
avtFLASHFileFormat(const char *, DBOptionsAttributes *);
virtual ~avtFLASHFileFormat();
virtual bool HasInvariantMetaData(void) const { return false; };
virtual bool HasInvariantSIL(void) const { return false; };
virtual const char *GetType(void) { return "FLASH"; };
virtual void FreeUpResources(void);
virtual void ActivateTimestep(void);
int GetCycle();
double GetTime();
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 *);
protected:
virtual void PopulateDatabaseMetaData(avtDatabaseMetaData *);
void ReadAllMetaData();
void BuildDomainNesting();
void ReadSimulationParameters(hid_t file_id, bool timeAndCycleOnly = false);
void ReadBlockStructure();
void ReadBlockExtents();
void ReadRefinementLevels();
void ReadUnknownNames();
void DetermineGlobalLogicalExtentsForAllBlocks();
void ReadParticleAttributes();
// FLASH3 support
void ReadParticleAttributes_FLASH3();
void ReadVersionInfo(hid_t file_id);
void ReadIntegerScalars(hid_t file_id);
void ReadRealScalars(hid_t file_id);
void ReadParticleVar(hid_t pointId, const char *, double *);
// HDF5 lib initialization
void InitializeHDF5();
void FinalizeHDF5();
vtkPolyData* GetMortonCurve();
vtkPolyData* GetMortonCurveSubset(int domain);
void ReadNodeTypes();
void ReadCoordinates();
void ReadProcessorNumbers();
protected:
struct SimParams
{
int total_blocks;
double time;
double timestep;
double redshift;
int nsteps;
int nxb;
int nyb;
int nzb;
};
struct Block
{
int ID;
int level;
int nodetype;
double coords[3];
int procnum;
int parentID;
int childrenIDs[8];
int neighborIDs[6];
double minSpatialExtents[3];
double maxSpatialExtents[3];
int minGlobalLogicalExtents[3];
int maxGlobalLogicalExtents[3];
void Print(ostream&);
};
// FLASH3 support
struct IntegerScalars
{
char name[20];
int value;
};
struct RealScalars
{
char name[20];
double value;
};
// Since 2 "file format version"s (FFV) for FLASH3, need to read "sim info"
// structure to read the FFV directly
struct sim_info_t
{
int file_format_version;
char setup_call[400];
char file_creation_time[80];
char flash_version[80];
char build_date[80];
char build_dir[80];
char build_machine[80];
char cflags[400];
char fflags[400];
char setup_time_stamp[80];
char build_time_stamp[80];
};
protected:
static int objcnt;
std::string filename;
int dimension;
int numBlocks;
int numLevels;
int numProcessors;
bool file_has_procnum;
static const int LEAF_NODE = 1;
int numLeafBlocks;
int numParticles;
int fileFormatVersion;
std::string particleHDFVarName;
hid_t fileId;
SimParams simParams;
sim_info_t simInfo;
std::vector<Block> blocks;
int numChildrenPerBlock;
int numNeighborsPerBlock;
int block_ndims[3];
int block_zdims[3];
double minSpatialExtents[3];
double maxSpatialExtents[3];
std::vector<std::string> varNames;
std::vector<std::string> particleVarNames;
std::vector<hid_t> particleVarTypes;
std::map<std::string,int> particleOriginalIndexMap;
std::vector<int> leafBlocks;
std::vector<int> patchesPerLevel;
std::vector<int> visitIdToFLASHId;
std::vector<int> FLASHIdToVisitId;
bool showProcessors;
bool newStyleCurves;
bool addStructuredDomainBoundaries;
};
#endif
|
