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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
|
1 //-------------------------------------------------------------------------
2 // Filename : NCHelper.hpp
3 //
4 // Purpose : Climate NC file helper
5 //
6 // Creator : Danqing Wu
7 //-------------------------------------------------------------------------
8
9 #ifndef NCHELPER_HPP
10 #define NCHELPER_HPP
11
12 #include "ReadNC.hpp"
13
14 #ifdef WIN32
15 #ifdef size_t
16 #undef size_t
17 #endif
18 #endif
19
20 namespace moab
21 {
22
23 //! Helper class to isolate reading of several different nc file formats
24 class NCHelper
25 {
26 public:
27 NCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
28 : _readNC( readNC ), _fileId( fileId ), _opts( opts ), _fileSet( fileSet ), nTimeSteps( 0 ), nLevels( 1 ),
29 tDim( -1 ), levDim( -1 )
30 {
31 }
32 virtual ~NCHelper() {}
33
34 //! Get appropriate format to read the file
35 static ReadNC::NCFormatType get_nc_format( ReadNC* readNC, int fileId );
36
37 //! Get appropriate format to read the file
38 static std::string get_default_ncformat_options( ReadNC::NCFormatType format );
39
40 //! Get appropriate helper instance for ReadNC class
41 static NCHelper* get_nc_helper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet );
42
43 //! Interfaces to be implemented in child classes
44 virtual ErrorCode init_mesh_vals() = 0;
45 virtual ErrorCode check_existing_mesh() = 0;
46 virtual ErrorCode create_mesh( Range& faces ) = 0;
47 virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums ) = 0;
48 virtual std::string get_mesh_type_name() = 0;
49
50 //! Create NC conventional tags
51 ErrorCode create_conventional_tags( const std::vector< int >& tstep_nums );
52
53 //! Update time tag values if timesteps spread across files
54 ErrorCode update_time_tag_vals();
55
56 // An object to hold vertex coordinates, and an operator
57 // for storing them in a STL tree-based container. use a tolerance saved somewhere as 1.e-12
58 class Node3D
59 {
60 public:
61 double coords[3];
62 bool operator<( const Node3D& ) const;
63 Node3D( double x, double y, double z )
64 {
65 coords[0] = x;
66 coords[1] = y;
67 coords[2] = z;
68 }
69 };
70
71 protected:
72 //! Separate set and non-set variables (common to scd mesh and ucd mesh)
73 ErrorCode read_variables_setup( std::vector< std::string >& var_names,
74 std::vector< int >& tstep_nums,
75 std::vector< ReadNC::VarData >& vdatas,
76 std::vector< ReadNC::VarData >& vsetdatas );
77
78 //! Read set variables (common to scd mesh and ucd mesh)
79 ErrorCode read_variables_to_set( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
80
81 ErrorCode read_coordinate( const char* var_name, int lmin, int lmax, std::vector< double >& cvals );
82
83 ErrorCode get_tag_to_set( ReadNC::VarData& var_data, int tstep_num, Tag& tagh );
84
85 ErrorCode get_tag_to_nonset( ReadNC::VarData& var_data, int tstep_num, Tag& tagh, int num_lev );
86
87 //! Create a character string attString of attMap. with '\0'
88 //! terminating each attribute name, ';' separating the data type
89 //! and value, and ';' separating one name/data type/value from
90 //! the next'. attLen stores the end position for each name/data
91 //! type/ value.
92 ErrorCode create_attrib_string( const std::map< std::string, ReadNC::AttData >& attMap,
93 std::string& attString,
94 std::vector< int >& attLen );
95
96 //! For a dimension that does not have a corresponding coordinate variable (e.g. ncol for
97 //! HOMME), create a dummy variable with a sparse tag to store the dimension length
98 ErrorCode create_dummy_variables();
99
100 private:
101 //! Used by read_variables_to_set()
102 ErrorCode read_variables_to_set_allocate( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
103
104 protected:
105 //! Allow NCHelper to directly access members of ReadNC
106 ReadNC* _readNC;
107
108 //! Cache some information from ReadNC
109 int _fileId;
110 const FileOptions& _opts;
111 EntityHandle _fileSet;
112
113 //! Dimensions of time and level
114 int nTimeSteps, nLevels;
115
116 //! Values for time and level
117 std::vector< double > tVals, levVals;
118
119 //! Dimension numbers for time and level
120 int tDim, levDim;
121
122 //! Ignored variables
123 std::set< std::string > ignoredVarNames;
124
125 //! Dummy variables
126 std::set< std::string > dummyVarNames;
127 };
128
129 //! Child helper class for scd mesh, e.g. CAM_EL or CAM_FV
130 class ScdNCHelper : public NCHelper
131 {
132 public:
133 ScdNCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
134 : NCHelper( readNC, fileId, opts, fileSet ), iDim( -1 ), jDim( -1 ), iCDim( -1 ), jCDim( -1 )
135 {
136 for( unsigned int i = 0; i < 6; i++ )
137 {
138 gDims[i] = -1;
139 lDims[i] = -1;
140 gCDims[i] = -1;
141 lCDims[i] = -1;
142 }
143
144 locallyPeriodic[0] = locallyPeriodic[1] = locallyPeriodic[2] = 0;
145 globallyPeriodic[0] = globallyPeriodic[1] = globallyPeriodic[2] = 0;
146 }
147 virtual ~ScdNCHelper() {}
148
149 private:
150 //! Implementation of NCHelper::check_existing_mesh()
151 virtual ErrorCode check_existing_mesh();
152 //! Implementation of NCHelper::create_mesh()
153 virtual ErrorCode create_mesh( Range& faces );
154 //! Implementation of NCHelper::read_variables()
155 virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
156
157 //! Read non-set variables for scd mesh
158 ErrorCode read_scd_variables_to_nonset_allocate( std::vector< ReadNC::VarData >& vdatas,
159 std::vector< int >& tstep_nums );
160 ErrorCode read_scd_variables_to_nonset( std::vector< ReadNC::VarData >& vdatas, std::vector< int >& tstep_nums );
161
162 //! Create COORDS tag for quads coordinate
163 ErrorCode create_quad_coordinate_tag();
164
165 template < typename T >
166 void kji_to_jik( size_t ni, size_t nj, size_t nk, void* dest, T* source )
167 {
168 size_t nik = ni * nk, nij = ni * nj;
169 T* tmp_data = reinterpret_cast< T* >( dest );
170 for( std::size_t j = 0; j != nj; j++ )
171 for( std::size_t i = 0; i != ni; i++ )
172 for( std::size_t k = 0; k != nk; k++ )
173 tmp_data[j * nik + i * nk + k] = source[k * nij + j * ni + i];
174 }
175
176 protected:
177 //! Dimensions of global grid in file
178 int gDims[6];
179
180 //! Dimensions of my local part of grid
181 int lDims[6];
182
183 //! Center dimensions of global grid in file
184 int gCDims[6];
185
186 //! Center dimensions of my local part of grid
187 int lCDims[6];
188
189 //! Values for i/j
190 std::vector< double > ilVals, jlVals;
191
192 //! Center values for i/j
193 std::vector< double > ilCVals, jlCVals;
194
195 //! Dimension numbers for i/j
196 int iDim, jDim;
197
198 //! Center dimension numbers for i/j
199 int iCDim, jCDim;
200
201 //! Whether mesh is locally periodic in i or j or k
202 int locallyPeriodic[3];
203
204 //! Whether mesh is globally periodic in i or j or k
205 int globallyPeriodic[3];
206 };
207
208 //! Child helper class for ucd mesh, e.g. CAM_SE (HOMME) or MPAS
209 class UcdNCHelper : public NCHelper
210 {
211 public:
212 UcdNCHelper( ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet )
213 : NCHelper( readNC, fileId, opts, fileSet ), nCells( 0 ), nEdges( 0 ), nVertices( 0 ), nLocalCells( 0 ),
214 nLocalEdges( 0 ), nLocalVertices( 0 ), cDim( -1 ), eDim( -1 ), vDim( -1 )
215 {
216 }
217 virtual ~UcdNCHelper() {}
218
219 private:
220 //! Implementation of NCHelper::read_variables()
221 virtual ErrorCode read_variables( std::vector< std::string >& var_names, std::vector< int >& tstep_nums );
222
223 //! Read non-set variables for ucd mesh (implemented differently in child classes)
224 virtual ErrorCode read_ucd_variables_to_nonset_allocate( std::vector< ReadNC::VarData >& vdatas,
225 std::vector< int >& tstep_nums ) = 0;
226 #ifdef MOAB_HAVE_PNETCDF
227 virtual ErrorCode read_ucd_variables_to_nonset_async( std::vector< ReadNC::VarData >& vdatas,
228 std::vector< int >& tstep_nums ) = 0;
229 #else
230 virtual ErrorCode read_ucd_variables_to_nonset( std::vector< ReadNC::VarData >& vdatas,
231 std::vector< int >& tstep_nums ) = 0;
232 #endif
233
234 protected:
235 //! This version takes as input the moab range, from which we actually need just the
236 //! size of each sequence, for a proper transpose of the data
237 template < typename T >
238 void kji_to_jik_stride( size_t, size_t nj, size_t nk, void* dest, T* source, Range& localGid )
239 {
240 std::size_t idxInSource = 0; // Position of the start of the stride
241 // For each subrange, we will transpose a matrix of size
242 // subrange*nj*nk (subrange takes the role of ni)
243 T* tmp_data = reinterpret_cast< T* >( dest );
244 for( Range::pair_iterator pair_iter = localGid.pair_begin(); pair_iter != localGid.pair_end(); ++pair_iter )
245 {
246 std::size_t size_range = pair_iter->second - pair_iter->first + 1;
247 std::size_t nik = size_range * nk, nij = size_range * nj;
248 for( std::size_t j = 0; j != nj; j++ )
249 for( std::size_t i = 0; i != size_range; i++ )
250 for( std::size_t k = 0; k != nk; k++ )
251 tmp_data[idxInSource + j * nik + i * nk + k] =
252 source[idxInSource + k * nij + j * size_range + i];
253 idxInSource += ( size_range * nj * nk );
254 }
255 }
256
257 //! Dimensions of global grid in file
258 int nCells;
259 int nEdges;
260 int nVertices;
261
262 //! Dimensions of my local part of grid
263 int nLocalCells;
264 int nLocalEdges;
265 int nLocalVertices;
266
267 //! Coordinate values for vertices
268 std::vector< double > xVertVals, yVertVals, zVertVals;
269
270 //! Dimension numbers for nCells, nEdges and nVertices
271 int cDim, eDim, vDim;
272
273 //! Local global ID for cells, edges and vertices
274 Range localGidCells, localGidEdges, localGidVerts;
275 };
276
277 } // namespace moab
278
279 #endif
1.9.1.