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