MOAB: Mesh Oriented datABase  (version 5.4.0)
ReadNCDF.hpp
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00001 /**
00002  * MOAB, a Mesh-Oriented datABase, is a software component for creating,
00003  * storing and accessing finite element mesh data.
00004  *
00005  * Copyright 2004 Sandia Corporation.  Under the terms of Contract
00006  * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
00007  * retains certain rights in this software.
00008  *
00009  * This library is free software; you can redistribute it and/or
00010  * modify it under the terms of the GNU Lesser General Public
00011  * License as published by the Free Software Foundation; either
00012  * version 2.1 of the License, or (at your option) any later version.
00013  *
00014  */
00015 
00016 //-------------------------------------------------------------------------
00017 // Filename      : ReadNCDF.hpp
00018 //
00019 // Purpose       : ExodusII reader
00020 //
00021 // Special Notes : Lots of code taken from verde implementation
00022 //
00023 // Creator       : Tim Tautges & Corey Ernst
00024 //
00025 // Date          : 3/02
00026 //
00027 // Owner         : Tim Tautges & Corey Ernst
00028 //-------------------------------------------------------------------------
00029 
00030 #ifndef READNCDF_HPP
00031 #define READNCDF_HPP
00032 
00033 #ifndef IS_BUILDING_MB
00034 //#error "ReadNCDF.hpp isn't supposed to be included into an application"
00035 #endif
00036 
00037 #include <vector>
00038 #include <string>
00039 
00040 #include "moab/Forward.hpp"
00041 #include "moab/ReaderIface.hpp"
00042 #include "moab/ExoIIInterface.hpp"
00043 #include "moab/Range.hpp"
00044 
00045 namespace moab
00046 {
00047 
00048 class ReadUtilIface;
00049 
00050 struct ReadBlockData
00051 {
00052     int blockId;
00053     int startExoId;
00054     EntityHandle startMBId;
00055     int numElements;
00056     bool reading_in;
00057     ExoIIElementType elemType;
00058     std::vector< EntityHandle > polys;  // used only if elem type is polyhedra or polygons
00059                                         // because the order has to be maintained
00060 };
00061 
00062 // these are for polyhedra only
00063 struct ReadFaceBlockData
00064 {
00065     int faceBlockId;
00066     int startExoId;
00067     int numElements;
00068     bool reading_in;
00069     // ExoIIElementType elemType; should be polygons
00070 };
00071 
00072 //! Output Exodus File for VERDE
00073 class ReadNCDF : public ReaderIface
00074 {
00075 
00076   public:
00077     static ReaderIface* factory( Interface* );
00078 
00079     void tokenize( const std::string& str, std::vector< std::string >& tokens, const char* delimiters );
00080 
00081     //! load an ExoII file
00082     ErrorCode load_file( const char* file_name,
00083                          const EntityHandle* file_set,
00084                          const FileOptions& opts,
00085                          const SubsetList* subset_list = 0,
00086                          const Tag* file_id_tag        = 0 );
00087 
00088     ErrorCode read_tag_values( const char* file_name,
00089                                const char* tag_name,
00090                                const FileOptions& opts,
00091                                std::vector< int >& tag_values_out,
00092                                const SubsetList* subset_list = 0 );
00093 
00094     //! Constructor
00095     ReadNCDF( Interface* impl = NULL );
00096 
00097     //! Destructor
00098     virtual ~ReadNCDF();
00099 
00100     // update the coords for deformed mesh according to FileOptions
00101     ErrorCode update( const char* exodus_file_name,
00102                       const FileOptions& opts,
00103                       const int num_blocks,
00104                       const int* blocks_to_load,
00105                       const EntityHandle file_set );
00106 
00107   private:
00108     ReadUtilIface* readMeshIface;
00109 
00110     bool dimension_exists( const char* attrib_name );
00111 
00112     void reset();
00113 
00114     //! read the header from the ExoII file
00115     ErrorCode read_exodus_header();
00116 
00117     //! read the nodes
00118     ErrorCode read_nodes( const Tag* file_id_tag );
00119 
00120     // face blocks for polyhedra
00121     ErrorCode read_face_blocks_headers();  // all of them?
00122 
00123     //! read block headers, containing info about element type, number, etc.
00124     ErrorCode read_block_headers( const int* blocks_to_load, const int num_blocks );
00125 
00126     // these are needed only when polyhedra are present
00127     ErrorCode read_polyhedra_faces();
00128 
00129     //! read the element blocks
00130     ErrorCode read_elements( const Tag* file_id_tag );
00131 
00132     //! read in the global element ids
00133     ErrorCode read_global_ids();
00134 
00135     //! read the nodesets into meshsets
00136     ErrorCode read_nodesets();
00137 
00138     //! read the sidesets (does nothing for now)
00139     ErrorCode read_sidesets();
00140 
00141     //! exodus file bound to this object
00142     int exodus_file();
00143 
00144     //! number of dimensions in this exo file
00145     int number_dimensions();
00146 
00147     //! map a character exodusII element type to a TSTT type & topology
00148     ErrorCode get_type( char* exo_element_type, EntityType& elem_type );
00149 
00150     ErrorCode get_type( EntityType& elem_type, std::string& exo_element_type );
00151 
00152     /*
00153     int get_int_tag(const MB_MeshSet *this_ms,
00154                     const TagHandle tag_id);
00155    */
00156 
00157     // qa record stuff
00158     ErrorCode read_qa_records( EntityHandle file_set );
00159     ErrorCode read_qa_information( std::vector< std::string >& qa_record_list );
00160 
00161     ErrorCode read_qa_string( char* string, int record_number, int record_position );
00162 
00163     ErrorCode create_ss_elements( int* element_ids,
00164                                   int* side_list,
00165                                   int num_sides,
00166                                   int num_dist_factors,
00167                                   std::vector< EntityHandle >& entities_to_add,
00168                                   std::vector< EntityHandle >& reverse_entities,
00169                                   std::vector< double >& dist_factor_vector,
00170                                   int ss_seq_id );
00171 
00172     ErrorCode find_side_element_type( const int element_id,
00173                                       ExoIIElementType& type,
00174                                       ReadBlockData& block_data,
00175                                       int& df_index,
00176                                       int side_id );
00177 
00178     /* ErrorCode assign_block_ids_to_ssets(EntityHandle ss_handle,
00179                                             MB_MeshSet *ss_mesh_set);
00180                                             */
00181 
00182     //! creates an element with the given connectivity
00183     ErrorCode create_sideset_element( const std::vector< EntityHandle >&, EntityType, EntityHandle&, int& );
00184 
00185     int get_number_nodes( EntityHandle handle );
00186 
00187     //------------member variables ------------//
00188 
00189     //! interface instance
00190     Interface* mdbImpl;
00191 
00192     int ncFile;  // netcdf/exodus file
00193 
00194     int CPU_WORD_SIZE;
00195     int IO_WORD_SIZE;
00196 
00197     //! int to offset vertex ids with
00198     int vertexOffset;
00199 
00200     //! file name
00201     std::string exodusFile;
00202 
00203     //! number of nodes in the current exoII file
00204     int numberNodes_loading;
00205 
00206     //! number of elements in the current exoII file
00207     int numberElements_loading;
00208 
00209     //! number of blocks in the current exoII file
00210     int numberElementBlocks_loading;
00211 
00212     //! number of face blocks in the current exoII file (used for polyhedra)
00213     int numberFaceBlocks_loading;
00214 
00215     //! number of nodesets in the current exoII file
00216     int numberNodeSets_loading;
00217 
00218     //! number of sidesets in the current exoII file
00219     int numberSideSets_loading;
00220 
00221     int numberDimensions_loading;
00222 
00223     //! Meshset Handle for the mesh that is currently being read
00224     EntityHandle mCurrentMeshHandle;
00225 
00226     // keeps track of the exodus ids of the elements and nodes just loaded
00227     std::vector< char > nodesInLoadedBlocks;
00228     // note- vector<bool> has limited capabilities
00229 
00230     // vector of blocks that are loading
00231     std::vector< ReadBlockData > blocksLoading;
00232 
00233     std::vector< EntityHandle > polyfaces;  // the order is maintained with this for polyhedra
00234 
00235     // vector of face blocks that are loading : these are for polyhedra blocks
00236     std::vector< ReadFaceBlockData > faceBlocksLoading;
00237 
00238     //! Cached tags for reading.  Note that all these tags are defined when the
00239     //! core is initialized.
00240     Tag mMaterialSetTag;
00241     Tag mDirichletSetTag;
00242     Tag mNeumannSetTag;
00243     Tag mHasMidNodesTag;
00244     Tag mDistFactorTag;
00245     Tag mGlobalIdTag;
00246     Tag mQaRecordTag;
00247 
00248     int max_line_length, max_str_length;
00249 
00250     //! range of entities in initial mesh, before this read
00251     Range initRange;
00252 };
00253 
00254 // inline functions
00255 inline int ReadNCDF::number_dimensions()
00256 {
00257     return numberDimensions_loading;
00258 }
00259 
00260 }  // namespace moab
00261 
00262 #endif
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