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
|
/*****************************************************************************
*
* 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.
*
*****************************************************************************/
// ************************************************************************* //
// avtChomboFileFormat.h //
// ************************************************************************* //
#ifndef AVT_Chombo_FILE_FORMAT_H
#define AVT_Chombo_FILE_FORMAT_H
#include <avtSTMDFileFormat.h>
#include <Expression.h>
#include <vector>
#include <list>
// 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>
struct {
int i;
int j;
} typedef intvect2d;
struct {
int i;
int j;
int k;
} typedef intvect3d;
struct {
intvect2d lo;
intvect2d hi;
} typedef box2d;
struct{
intvect3d lo;
intvect3d hi;
} typedef box3d;
union
{
box2d b2;
box3d b3;
} typedef box;
struct {
double x;
double y;
} typedef doublevect2d;
struct {
double x;
double y;
double z;
} typedef doublevect3d;
union
{
doublevect2d dv2;
doublevect3d dv3;
} typedef doublevect;
class DBOptionsAttributes;
// ****************************************************************************
// Class: avtChomboFileFormat
//
// Purpose:
// Reads in Chombo files as a plugin to VisIt.
//
// Programmer: Hank Childs
// Creation: Thu Jan 19 11:17:14 PDT 2006
//
// Modifications:
//
// Hank Childs, Mon Jun 19 16:44:06 PDT 2006
// Add support for ghost zones.
//
// Brad Whitlock, Mon Sep 25 13:54:59 PST 2006
// I added some fixes for getting cycle,time and for time-varying metadata.
//
// Gunther H. Weber, Tue Aug 7 15:56:32 PDT 2007
// Added material support
//
// Hank Childs, Mon Oct 8 17:17:24 PDT 2007
// Added options for reading.
//
// Gunther H. Weber, Mon Oct 22 11:22:35 PDT 2007
// Added information about problem domain [low|hi]Prob[I|J|K] needed
// to figure out whether a ghost zone is external to the problem.
//
// Gunther H. Weber, Mon Mar 24 20:45:05 PDT 2008
// Added support for node centered Chombo files.
//
// Gunther H. Weber, Tue Apr 15 17:43:30 PDT 2008
// Add support to automatically import a coordinate mapping file via conn_cmfe
//
// Hank Childs, Sun Jan 25 15:38:50 PST 2009
// Improve support for ghost data.
//
// Gunther H. Weber, Wed Jun 10 18:25:34 PDT 2009
// Added support for particle data in Chombo files
//
// Gunther H. Weber, Tue Sep 15 11:25:21 PDT 2009
// Added support for 3D mappings for 2D files
//
// Gunther H. Weber, Thu Jun 17 10:10:17 PDT 2010
// Added ability to connect particle mesh based on polymer_id and
// particle_nid
//
// ****************************************************************************
class avtChomboFileFormat : public avtSTMDFileFormat
{
public:
avtChomboFileFormat(const char *, DBOptionsAttributes*);
virtual ~avtChomboFileFormat();
virtual const char *GetType(void) { return "Chombo"; };
virtual void FreeUpResources(void);
virtual void ActivateTimestep(void);
virtual vtkDataSet *GetMesh(int, const char *);
virtual vtkDataArray *GetVar(int, const char *);
virtual vtkDataArray *GetVectorVar(int, const char *);
virtual void PopulateDatabaseMetaData(avtDatabaseMetaData *);
virtual void *GetAuxiliaryData(const char *var, int,
const char *type, void *args,
DestructorFunction &);
void *GetMaterial(const char *var, int patch,
const char *type,
DestructorFunction &df);
protected:
bool initializedReader;
int dimension;
hid_t file_handle;
std::vector<std::string> varnames;
int nMaterials;
bool hasParticles;
bool connectParticles;
std::vector<std::string> particleVarnames;
double dtime;
int cycle;
//int max_level;
int num_levels;
bool nodeCentered;
std::vector<int> numGhosts;
std::vector<int> patchesPerLevel;
std::vector<int> refinement_ratio;
std::vector<double> dx;
std::list<Expression*> expressions;
bool allowedToUseGhosts;
bool fileContainsGhosts;
bool enableOnlyRootLevel;
bool enableOnlyExplicitMaterials;
bool checkForMappingFile;
bool mappingFileExists;
bool mappingIs3D;
std::vector<int> lowProbI;
std::vector<int> hiProbI;
std::vector<int> lowProbJ;
std::vector<int> hiProbJ;
std::vector<int> lowProbK;
std::vector<int> hiProbK;
std::vector<int> lowI;
std::vector<int> hiI;
std::vector<int> lowJ;
std::vector<int> hiJ;
std::vector<int> lowK;
std::vector<int> hiK;
double probLo[3];
double aspectRatio[3];
void InitializeReader(void);
void GetLevelAndLocalPatchNumber(int global_patch,
int &level, int &local_patch) const;
void CalculateDomainNesting(void);
virtual int GetCycle(void);
virtual double GetTime(void);
virtual int GetCycleFromFilename(const char *f) const;
virtual bool HasInvariantMetaData(void) const { return false; };
virtual bool HasInvariantSIL(void) const { return false; };
};
#endif
|
