ReadCGNS.cpp

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/**
 * \class ReadCGNS
 * \brief Template for writing a new reader in MOAB
 *
 */
 
#include "ReadCGNS.hpp"
#include "Internals.hpp"
#include "moab/Interface.hpp"
#include "moab/ReadUtilIface.hpp"
#include "moab/Range.hpp"
#include "moab/FileOptions.hpp"
#include "MBTagConventions.hpp"
#include "MBParallelConventions.h"
#include "moab/CN.hpp"
 
#include <cstdio>
#include <cassert>
#include <cerrno>
#include <map>
#include <set>
 
#include <iostream>
#include <cmath>
 
namespace moab
{
 
ReaderIface* ReadCGNS::factory( Interface* iface )
{
 return new ReadCGNS( iface );
}
 
ReadCGNS::ReadCGNS( Interface* impl ) : fileName( NULL ), mesh_dim( 0 ), mbImpl( impl ), globalId( 0 ), boundary( 0 )
{
 mbImpl->query_interface( readMeshIface );
}
 
ReadCGNS::~ReadCGNS()
{
 if( readMeshIface )
 {
 mbImpl->release_interface( readMeshIface );
 readMeshIface = 0;
 }
}
 
ErrorCode ReadCGNS::read_tag_values( const char* /* file_name */,
 const char* /* tag_name */,
 const FileOptions& /* opts */,
 std::vector< int >& /* tag_values_out */,
 const SubsetList* /* subset_list */ )
{
 return MB_NOT_IMPLEMENTED;
}
 
ErrorCode ReadCGNS::load_file( const char* filename,
 const EntityHandle* /*file_set*/,
 const FileOptions& opts,
 const ReaderIface::SubsetList* subset_list,
 const Tag* file_id_tag )
{
 int num_material_sets = 0;
 const int* material_set_list = 0;
 
 if( subset_list )
 {
 if( subset_list->tag_list_length > 1 && !strcmp( subset_list->tag_list[0].tag_name, MATERIAL_SET_TAG_NAME ) )
 {
 MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "CGNS supports subset read only by material ID" );
 }
 material_set_list = subset_list->tag_list[0].tag_values;
 num_material_sets = subset_list->tag_list[0].num_tag_values;
 }
 
 ErrorCode result;
 
 geomSets.clear();
 globalId = mbImpl->globalId_tag();
 
 // Create set for more convenient check for material set ids
 std::set< int > blocks;
 for( const int* mat_set_end = material_set_list + num_material_sets; material_set_list != mat_set_end;
 ++material_set_list )
 blocks.insert( *material_set_list );
 
 // Map of ID->handle for nodes
 std::map< long, EntityHandle > node_id_map;
 
 // Save filename to member variable so we don't need to pass as an argument
 // to called functions
 fileName = filename;
 
 // Process options; see src/FileOptions.hpp for API for FileOptions class, and
 // doc/metadata_info.doc for a description of various options used by some of the readers in
 // MOAB
 result = process_options( opts );MB_CHK_SET_ERR( result, fileName << ": problem reading options" );
 
 // Open file
 int filePtr = 0;
 
 cg_open( filename, CG_MODE_READ, &filePtr );
 
 if( filePtr <= 0 )
 {
 MB_SET_ERR( MB_FILE_DOES_NOT_EXIST, fileName << ": fopen returned error" );
 }
 
 // Read number of verts, elements, sets
 long num_verts = 0, num_elems = 0, num_sets = 0;
 int num_bases = 0, num_zones = 0, num_sections = 0;
 
 char zoneName[128];
 cgsize_t size[3];
 
 mesh_dim = 3; // Default to 3D
 
 // Read number of bases;
 cg_nbases( filePtr, &num_bases );
 
 if( num_bases > 1 )
 {
 MB_SET_ERR( MB_NOT_IMPLEMENTED, fileName << ": support for number of bases > 1 not implemented" );
 }
 
 for( int indexBase = 1; indexBase <= num_bases; ++indexBase )
 {
 // Get the number of zones/blocks in current base.
 cg_nzones( filePtr, indexBase, &num_zones );
 
 if( num_zones > 1 )
 {
 MB_SET_ERR( MB_NOT_IMPLEMENTED, fileName << ": support for number of zones > 1 not implemented" );
 }
 
 for( int indexZone = 1; indexZone <= num_zones; ++indexZone )
 {
 // Get zone name and size.
 cg_zone_read( filePtr, indexBase, indexZone, zoneName, size );
 
 // Read number of sections/Parts in current zone.
 cg_nsections( filePtr, indexBase, indexZone, &num_sections );
 
 num_verts = size[0];
 num_elems = size[1];
 num_sets = num_sections;
 
 std::cout << "\nnumber of nodes = " << num_verts;
 std::cout << "\nnumber of elems = " << num_elems;
 std::cout << "\nnumber of parts = " << num_sets << std::endl;
 
 // //////////////////////////////////
 // Read Nodes
 
 // Allocate nodes; these are allocated in one shot, get contiguous handles starting with
 // start_handle, and the reader is passed back double*'s pointing to MOAB's native
 // storage for vertex coordinates for those verts
 std::vector< double* > coord_arrays;
 EntityHandle handle = 0;
 result = readMeshIface->get_node_coords( 3, num_verts, MB_START_ID, handle, coord_arrays );MB_CHK_SET_ERR( result, fileName << ": Trouble reading vertices" );
 
 // Fill in vertex coordinate arrays
 cgsize_t beginPos = 1, endPos = num_verts;
 
 // Read nodes coordinates.
 cg_coord_read( filePtr, indexBase, indexZone, "CoordinateX", RealDouble, &beginPos, &endPos,
 coord_arrays[0] );
 cg_coord_read( filePtr, indexBase, indexZone, "CoordinateY", RealDouble, &beginPos, &endPos,
 coord_arrays[1] );
 cg_coord_read( filePtr, indexBase, indexZone, "CoordinateZ", RealDouble, &beginPos, &endPos,
 coord_arrays[2] );
 
 // CGNS seems to always include the Z component, even if the mesh is 2D.
 // Check if Z is zero and determine mesh dimension.
 // Also create the node_id_map data.
 double sumZcoord = 0.0;
 double eps = 1.0e-12;
 for( long i = 0; i < num_verts; ++i, ++handle )
 {
 int index = i + 1;
 
 node_id_map.insert( std::pair< long, EntityHandle >( index, handle ) ).second;
 
 sumZcoord += *( coord_arrays[2] + i );
 }
 if( std::abs( sumZcoord ) <= eps ) mesh_dim = 2;
 
 // Create reverse map from handle to id
 std::vector< int > ids( num_verts );
 std::vector< int >::iterator id_iter = ids.begin();
 std::vector< EntityHandle > handles( num_verts );
 std::vector< EntityHandle >::iterator h_iter = handles.begin();
 for( std::map< long, EntityHandle >::iterator i = node_id_map.begin(); i != node_id_map.end();
 ++i, ++id_iter, ++h_iter )
 {
 *id_iter = i->first;
 *h_iter = i->second;
 }
 // Store IDs in tags
 result = mbImpl->tag_set_data( globalId, &handles[0], num_verts, &ids[0] );
 if( MB_SUCCESS != result ) return result;
 if( file_id_tag )
 {
 result = mbImpl->tag_set_data( *file_id_tag, &handles[0], num_verts, &ids[0] );
 if( MB_SUCCESS != result ) return result;
 }
 ids.clear();
 handles.clear();
 
 // //////////////////////////////////
 // Read elements data
 
 EntityType ent_type;
 
 long section_offset = 0;
 
 // Define which mesh parts are volume families.
 // Mesh parts with volumeID[X] = 0 are boundary parts.
 std::vector< int > volumeID( num_sections, 0 );
 
 for( int section = 0; section < num_sections; ++section )
 {
 ElementType_t elemsType;
 int iparent_flag, nbndry;
 char sectionName[128];
 int verts_per_elem;
 
 int cgSection = section + 1;
 
 cg_section_read( filePtr, indexBase, indexZone, cgSection, sectionName, &elemsType, &beginPos, &endPos,
 &nbndry, &iparent_flag );
 
 size_t section_size = endPos - beginPos + 1;
 
 // Read element description in current section
 
 switch( elemsType )
 {
 case BAR_2:
 ent_type = MBEDGE;
 verts_per_elem = 2;
 break;
 case TRI_3:
 ent_type = MBTRI;
 verts_per_elem = 3;
 if( mesh_dim == 2 ) volumeID[section] = 1;
 break;
 case QUAD_4:
 ent_type = MBQUAD;
 verts_per_elem = 4;
 if( mesh_dim == 2 ) volumeID[section] = 1;
 break;
 case TETRA_4:
 ent_type = MBTET;
 verts_per_elem = 4;
 if( mesh_dim == 3 ) volumeID[section] = 1;
 break;
 case PYRA_5:
 ent_type = MBPYRAMID;
 verts_per_elem = 5;
 if( mesh_dim == 3 ) volumeID[section] = 1;
 break;
 case PENTA_6:
 ent_type = MBPRISM;
 verts_per_elem = 6;
 if( mesh_dim == 3 ) volumeID[section] = 1;
 break;
 case HEXA_8:
 ent_type = MBHEX;
 verts_per_elem = 8;
 if( mesh_dim == 3 ) volumeID[section] = 1;
 break;
 case MIXED:
 ent_type = MBMAXTYPE;
 verts_per_elem = 0;
 break;
 default:
 MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, fileName << ": Trouble determining element type" );
 }
 
 if( elemsType == TETRA_4 || elemsType == PYRA_5 || elemsType == PENTA_6 || elemsType == HEXA_8 ||
 elemsType == TRI_3 || elemsType == QUAD_4 || ( ( elemsType == BAR_2 ) && mesh_dim == 2 ) )
 {
 // Read connectivity into conn_array directly
 
 cgsize_t iparentdata;
 cgsize_t connDataSize;
 
 // Get number of entries on the connectivity list for this section
 cg_ElementDataSize( filePtr, indexBase, indexZone, cgSection, &connDataSize );
 
 // Need a temporary vector to later cast to conn_array.
 std::vector< cgsize_t > elemNodes( connDataSize );
 
 cg_elements_read( filePtr, indexBase, indexZone, cgSection, &elemNodes[0], &iparentdata );
 
 // //////////////////////////////////
 // Create elements, sets and tags
 
 create_elements( sectionName, file_id_tag, ent_type, verts_per_elem, section_offset, section_size,
 elemNodes );
 } // Homogeneous mesh type
 else if( elemsType == MIXED )
 {
 // We must first sort all elements connectivities into continuous vectors
 
 cgsize_t connDataSize;
 cgsize_t iparentdata;
 
 cg_ElementDataSize( filePtr, indexBase, indexZone, cgSection, &connDataSize );
 
 std::vector< cgsize_t > elemNodes( connDataSize );
 
 cg_elements_read( filePtr, indexBase, indexZone, cgSection, &elemNodes[0], &iparentdata );
 
 std::vector< cgsize_t > elemsConn_EDGE;
 std::vector< cgsize_t > elemsConn_TRI, elemsConn_QUAD;
 std::vector< cgsize_t > elemsConn_TET, elemsConn_PYRA, elemsConn_PRISM, elemsConn_HEX;
 cgsize_t count_EDGE, count_TRI, count_QUAD;
 cgsize_t count_TET, count_PYRA, count_PRISM, count_HEX;
 
 // First, get elements count for current section
 
 count_EDGE = count_TRI = count_QUAD = 0;
 count_TET = count_PYRA = count_PRISM = count_HEX = 0;
 
 int connIndex = 0;
 for( int i = beginPos; i <= endPos; i++ )
 {
 elemsType = ElementType_t( elemNodes[connIndex] );
 
 // Get current cell node count.
 cg_npe( elemsType, &verts_per_elem );
 
 switch( elemsType )
 {
 case BAR_2:
 count_EDGE += 1;
 break;
 case TRI_3:
 count_TRI += 1;
 break;
 case QUAD_4:
 count_QUAD += 1;
 break;
 case TETRA_4:
 count_TET += 1;
 break;
 case PYRA_5:
 count_PYRA += 1;
 break;
 case PENTA_6:
 count_PRISM += 1;
 break;
 case HEXA_8:
 count_HEX += 1;
 break;
 default:
 MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, fileName << ": Trouble determining element type" );
 }
 
 connIndex += ( verts_per_elem + 1 ); // Add one to skip next element descriptor
 }
 
 if( count_EDGE > 0 ) elemsConn_EDGE.resize( count_EDGE * 2 );
 if( count_TRI > 0 ) elemsConn_TRI.resize( count_TRI * 3 );
 if( count_QUAD > 0 ) elemsConn_QUAD.resize( count_QUAD * 4 );
 if( count_TET > 0 ) elemsConn_TET.resize( count_TET * 4 );
 if( count_PYRA > 0 ) elemsConn_PYRA.resize( count_PYRA * 5 );
 if( count_PRISM > 0 ) elemsConn_PRISM.resize( count_PRISM * 6 );
 if( count_HEX > 0 ) elemsConn_HEX.resize( count_HEX * 8 );
 
 // Grab mixed section elements connectivity
 
 int idx_edge, idx_tri, idx_quad;
 int idx_tet, idx_pyra, idx_prism, idx_hex;
 idx_edge = idx_tri = idx_quad = 0;
 idx_tet = idx_pyra = idx_prism = idx_hex = 0;
 
 connIndex = 0;
 for( int i = beginPos; i <= endPos; i++ )
 {
 elemsType = ElementType_t( elemNodes[connIndex] );
 
 // Get current cell node count.
 cg_npe( elemsType, &verts_per_elem );
 
 switch( elemsType )
 {
 case BAR_2:
 for( int j = 0; j < 2; ++j )
 elemsConn_EDGE[idx_edge + j] = elemNodes[connIndex + j + 1];
 idx_edge += 2;
 break;
 case TRI_3:
 for( int j = 0; j < 3; ++j )
 elemsConn_TRI[idx_tri + j] = elemNodes[connIndex + j + 1];
 idx_tri += 3;
 break;
 case QUAD_4:
 for( int j = 0; j < 4; ++j )
 elemsConn_QUAD[idx_quad + j] = elemNodes[connIndex + j + 1];
 idx_quad += 4;
 break;
 case TETRA_4:
 for( int j = 0; j < 4; ++j )
 elemsConn_TET[idx_tet + j] = elemNodes[connIndex + j + 1];
 idx_tet += 4;
 break;
 case PYRA_5:
 for( int j = 0; j < 5; ++j )
 elemsConn_PYRA[idx_pyra + j] = elemNodes[connIndex + j + 1];
 idx_pyra += 5;
 break;
 case PENTA_6:
 for( int j = 0; j < 6; ++j )
 elemsConn_PRISM[idx_prism + j] = elemNodes[connIndex + j + 1];
 idx_prism += 6;
 break;
 case HEXA_8:
 for( int j = 0; j < 8; ++j )
 elemsConn_HEX[idx_hex + j] = elemNodes[connIndex + j + 1];
 idx_hex += 8;
 break;
 default:
 MB_SET_ERR( MB_INDEX_OUT_OF_RANGE, fileName << ": Trouble determining element type" );
 }
 
 connIndex += ( verts_per_elem + 1 ); // Add one to skip next element descriptor
 }
 
 // //////////////////////////////////
 // Create elements, sets and tags
 
 if( count_EDGE > 0 )
 create_elements( sectionName, file_id_tag, MBEDGE, 2, section_offset, count_EDGE,
 elemsConn_EDGE );
 
 if( count_TRI > 0 )
 create_elements( sectionName, file_id_tag, MBTRI, 3, section_offset, count_TRI, elemsConn_TRI );
 
 if( count_QUAD > 0 )
 create_elements( sectionName, file_id_tag, MBQUAD, 4, section_offset, count_QUAD,
 elemsConn_QUAD );
 
 if( count_TET > 0 )
 create_elements( sectionName, file_id_tag, MBTET, 4, section_offset, count_TET, elemsConn_TET );
 
 if( count_PYRA > 0 )
 create_elements( sectionName, file_id_tag, MBPYRAMID, 5, section_offset, count_PYRA,
 elemsConn_PYRA );
 
 if( count_PRISM > 0 )
 create_elements( sectionName, file_id_tag, MBPRISM, 6, section_offset, count_PRISM,
 elemsConn_PRISM );
 
 if( count_HEX > 0 )
 create_elements( sectionName, file_id_tag, MBHEX, 8, section_offset, count_HEX, elemsConn_HEX );
 } // Mixed mesh type
 } // num_sections
 
 cg_close( filePtr );
 
 return result;
 } // indexZone for
 } // indexBase for
 
 return MB_SUCCESS;
}
 
ErrorCode ReadCGNS::create_elements( char* sectionName,
 const Tag* file_id_tag,
 const EntityType& ent_type,
 const int& verts_per_elem,
 long& section_offset,
 int elems_count,
 const std::vector< cgsize_t >& elemsConn )
{
 ErrorCode result;
 
 // Create the element sequence; passes back a pointer to the internal storage for connectivity
 // and the starting entity handle
 EntityHandle* conn_array;
 EntityHandle handle = 0;
 
 result = readMeshIface->get_element_connect( elems_count, verts_per_elem, ent_type, 1, handle, conn_array );MB_CHK_SET_ERR( result, fileName << ": Trouble reading elements" );
 
 if( sizeof( EntityHandle ) == sizeof( cgsize_t ) )
 {
 memcpy( conn_array, &elemsConn[0], elemsConn.size() * sizeof( EntityHandle ) );
 }
 else
 { // if CGNS is compiled without 64bit enabled
 std::vector< EntityHandle > elemsConnTwin( elemsConn.size(), 0 );
 for( int i = 0; i < elemsConn.size(); i++ )
 {
 elemsConnTwin[i] = static_cast< EntityHandle >( elemsConn[i] );
 }
 memcpy( conn_array, &elemsConnTwin[0], elemsConnTwin.size() * sizeof( EntityHandle ) );
 }
 
 // Notify MOAB of the new elements
 result = readMeshIface->update_adjacencies( handle, elems_count, verts_per_elem, conn_array );
 if( MB_SUCCESS != result ) return result;
 
 // //////////////////////////////////
 // Create sets and tags
 
 Range elements( handle, handle + elems_count - 1 );
 
 // Store element IDs
 
 std::vector< int > id_list( elems_count );
 
 // Add 1 to offset id to 1-based numbering
 for( cgsize_t i = 0; i < elems_count; ++i )
 id_list[i] = i + 1 + section_offset;
 section_offset += elems_count;
 
 create_sets( sectionName, file_id_tag, ent_type, elements, id_list, 0 );
 
 return MB_SUCCESS;
}
 
ErrorCode ReadCGNS::create_sets( char* sectionName,
 const Tag* file_id_tag,
 EntityType /*element_type*/,
 const Range& elements,
 const std::vector< int >& set_ids,
 int /*set_type*/ )
{
 ErrorCode result;
 
 result = mbImpl->tag_set_data( globalId, elements, &set_ids[0] );
 if( MB_SUCCESS != result ) return result;
 
 if( file_id_tag )
 {
 result = mbImpl->tag_set_data( *file_id_tag, elements, &set_ids[0] );
 if( MB_SUCCESS != result ) return result;
 }
 
 EntityHandle set_handle;
 
 Tag tag_handle;
 
 const char* setName = sectionName;
 
 mbImpl->tag_get_handle( setName, 1, MB_TYPE_INTEGER, tag_handle, MB_TAG_SPARSE | MB_TAG_CREAT );
 
 // Create set
 result = mbImpl->create_meshset( MESHSET_SET, set_handle );MB_CHK_SET_ERR( result, fileName << ": Trouble creating set" );
 
 //// Add dummy values to current set
 // std::vector<int> tags(set_ids.size(), 1);
 // result = mbImpl->tag_set_data(tag_handle, elements, &tags[0]);
 // if (MB_SUCCESS != result) return result;
 
 // Add them to the set
 result = mbImpl->add_entities( set_handle, elements );MB_CHK_SET_ERR( result, fileName << ": Trouble putting entities in set" );
 
 return MB_SUCCESS;
}
 
ErrorCode ReadCGNS::process_options( const FileOptions& opts )
{
 // Mark all options seen, to avoid compile warning on unused variable
 opts.mark_all_seen();
 
 return MB_SUCCESS;
}
 
} // namespace moab