ReadNCDF.hpp

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/**
 * MOAB, a Mesh-Oriented datABase, is a software component for creating,
 * storing and accessing finite element mesh data.
 *
 * Copyright 2004 Sandia Corporation.  Under the terms of Contract
 * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
 * retains certain rights in this software.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 */
 
//-------------------------------------------------------------------------
// Filename      : ReadNCDF.hpp
//
// Purpose       : ExodusII reader
//
// Special Notes : Lots of code taken from verde implementation
//
// Creator       : Tim Tautges & Corey Ernst
//
// Date          : 3/02
//
// Owner         : Tim Tautges & Corey Ernst
//-------------------------------------------------------------------------
 
#ifndef READNCDF_HPP
#define READNCDF_HPP
 
#ifndef IS_BUILDING_MB
//#error "ReadNCDF.hpp isn't supposed to be included into an application"
#endif
 
#include <vector>
#include <string>
 
#include "moab/Forward.hpp"
#include "moab/ReaderIface.hpp"
#include "moab/ExoIIInterface.hpp"
#include "moab/Range.hpp"
 
namespace moab
{
 
class ReadUtilIface;
 
struct ReadBlockData
{
    int blockId;
    int startExoId;
    EntityHandle startMBId;
    int numElements;
    bool reading_in;
    ExoIIElementType elemType;
    std::vector< EntityHandle > polys;  // used only if elem type is polyhedra or polygons
                                        // because the order has to be maintained
};
 
// these are for polyhedra only
struct ReadFaceBlockData
{
    int faceBlockId;
    int startExoId;
    int numElements;
    bool reading_in;
    // ExoIIElementType elemType; should be polygons
};
 
//! Output Exodus File for VERDE
class ReadNCDF : public ReaderIface
{
 
  public:
    static ReaderIface* factory( Interface* );
 
    void tokenize( const std::string& str, std::vector< std::string >& tokens, const char* delimiters );
 
    //! load an ExoII file
    ErrorCode load_file( const char* file_name,
                         const EntityHandle* file_set,
                         const FileOptions& opts,
                         const SubsetList* subset_list = 0,
                         const Tag* file_id_tag        = 0 );
 
    ErrorCode read_tag_values( const char* file_name,
                               const char* tag_name,
                               const FileOptions& opts,
                               std::vector< int >& tag_values_out,
                               const SubsetList* subset_list = 0 );
 
    //! Constructor
    ReadNCDF( Interface* impl = NULL );
 
    //! Destructor
    virtual ~ReadNCDF();
 
    // update the coords for deformed mesh according to FileOptions
    ErrorCode update( const char* exodus_file_name,
                      const FileOptions& opts,
                      const int num_blocks,
                      const int* blocks_to_load,
                      const EntityHandle file_set );
 
  private:
    ReadUtilIface* readMeshIface;
 
    bool dimension_exists( const char* attrib_name );
 
    void reset();
 
    //! read the header from the ExoII file
    ErrorCode read_exodus_header();
 
    //! read the nodes
    ErrorCode read_nodes( const Tag* file_id_tag );
 
    // face blocks for polyhedra
    ErrorCode read_face_blocks_headers();  // all of them?
 
    //! read block headers, containing info about element type, number, etc.
    ErrorCode read_block_headers( const int* blocks_to_load, const int num_blocks );
 
    // these are needed only when polyhedra are present
    ErrorCode read_polyhedra_faces();
 
    //! read the element blocks
    ErrorCode read_elements( const Tag* file_id_tag );
 
    //! read in the global element ids
    ErrorCode read_global_ids();
 
    //! read the nodesets into meshsets
    ErrorCode read_nodesets();
 
    //! read the sidesets (does nothing for now)
    ErrorCode read_sidesets();
 
    //! exodus file bound to this object
    int exodus_file();
 
    //! number of dimensions in this exo file
    int number_dimensions();
 
    //! map a character exodusII element type to a TSTT type & topology
    ErrorCode get_type( char* exo_element_type, EntityType& elem_type );
 
    ErrorCode get_type( EntityType& elem_type, std::string& exo_element_type );
 
    /*
    int get_int_tag(const MB_MeshSet *this_ms,
                    const TagHandle tag_id);
   */
 
    // qa record stuff
    ErrorCode read_qa_records( EntityHandle file_set );
    ErrorCode read_qa_information( std::vector< std::string >& qa_record_list );
 
    ErrorCode read_qa_string( char* string, int record_number, int record_position );
 
    ErrorCode create_ss_elements( int* element_ids,
                                  int* side_list,
                                  int num_sides,
                                  int num_dist_factors,
                                  std::vector< EntityHandle >& entities_to_add,
                                  std::vector< EntityHandle >& reverse_entities,
                                  std::vector< double >& dist_factor_vector,
                                  int ss_seq_id );
 
    ErrorCode find_side_element_type( const int element_id,
                                      ExoIIElementType& type,
                                      ReadBlockData& block_data,
                                      int& df_index,
                                      int side_id );
 
    /* ErrorCode assign_block_ids_to_ssets(EntityHandle ss_handle,
                                            MB_MeshSet *ss_mesh_set);
                                            */
 
    //! creates an element with the given connectivity
    ErrorCode create_sideset_element( const std::vector< EntityHandle >&, EntityType, EntityHandle&, int& );
 
    int get_number_nodes( EntityHandle handle );
 
    //------------member variables ------------//
 
    //! interface instance
    Interface* mdbImpl;
 
    int ncFile;  // netcdf/exodus file
 
    int CPU_WORD_SIZE;
    int IO_WORD_SIZE;
 
    //! int to offset vertex ids with
    int vertexOffset;
 
    //! file name
    std::string exodusFile;
 
    //! number of nodes in the current exoII file
    int numberNodes_loading;
 
    //! number of elements in the current exoII file
    int numberElements_loading;
 
    //! number of blocks in the current exoII file
    int numberElementBlocks_loading;
 
    //! number of face blocks in the current exoII file (used for polyhedra)
    int numberFaceBlocks_loading;
 
    //! number of nodesets in the current exoII file
    int numberNodeSets_loading;
 
    //! number of sidesets in the current exoII file
    int numberSideSets_loading;
 
    int numberDimensions_loading;
 
    //! Meshset Handle for the mesh that is currently being read
    EntityHandle mCurrentMeshHandle;
 
    // keeps track of the exodus ids of the elements and nodes just loaded
    std::vector< char > nodesInLoadedBlocks;
    // note- vector<bool> has limited capabilities
 
    // vector of blocks that are loading
    std::vector< ReadBlockData > blocksLoading;
 
    std::vector< EntityHandle > polyfaces;  // the order is maintained with this for polyhedra
 
    // vector of face blocks that are loading : these are for polyhedra blocks
    std::vector< ReadFaceBlockData > faceBlocksLoading;
 
    //! Cached tags for reading.  Note that all these tags are defined when the
    //! core is initialized.
    Tag mMaterialSetTag;
    Tag mDirichletSetTag;
    Tag mNeumannSetTag;
    Tag mHasMidNodesTag;
    Tag mDistFactorTag;
    Tag mGlobalIdTag;
    Tag mQaRecordTag;
 
    int max_line_length, max_str_length;
 
    //! range of entities in initial mesh, before this read
    Range initRange;
};
 
// inline functions
inline int ReadNCDF::number_dimensions()
{
    return numberDimensions_loading;
}
 
}  // namespace moab
 
#endif