Gmsh (http://www.geuz.org/gmsh) file reader. More...

#include <ReadGmsh.hpp>

Inheritance diagram for moab::ReadGmsh:

Collaboration diagram for moab::ReadGmsh:

Public Member Functions
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)
	Load mesh from a file.
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)
	Read tag values from a file.
	ReadGmsh (Interface *impl=NULL)
	Constructor.
virtual	~ReadGmsh ()
	Destructor.
Static Public Member Functions
static ReaderIface *	factory (Interface *)
	factory method
Private Member Functions
ErrorCode	create_elements (const GmshElemType &type, const std::vector< int > &elem_ids, const std::vector< int > &matl_ids, const std::vector< int > &geom_ids, const std::vector< int > &prtn_ids, const std::vector< EntityHandle > &connectivity, const Tag *file_id_tag)
	Create an element sequence.
ErrorCode	create_sets (EntityType element_type, const Range &elements, const std::vector< int > &set_ids, int set_type)
	Add elements to sets as dictated by grouping ID in file.
ErrorCode	create_geometric_topology ()
	NOT IMPLEMENTED Reconstruct parent-child relations for geometry sets from mesh connectivity.
Private Attributes
ReadUtilIface *	readMeshIface
Interface *	mdbImpl
	interface instance
Tag	globalId
Range	geomSets

Detailed Description

Gmsh (http://www.geuz.org/gmsh) file reader.

Author:: Jason Kraftcheck

Definition at line 33 of file ReadGmsh.hpp.

Constructor & Destructor Documentation

ReadGmsh::ReadGmsh ( Interface * impl = NULL )

Constructor.

Definition at line 49 of file ReadGmsh.cpp.

References mdbImpl, moab::Interface::query_interface(), and readMeshIface.

Referenced by factory().

                                    : mdbImpl( impl ), globalId( 0 )
{
    mdbImpl->query_interface( readMeshIface );
}

ReadGmsh::~ReadGmsh ( ) [virtual]

Destructor.

Definition at line 54 of file ReadGmsh.cpp.

References mdbImpl, readMeshIface, and moab::Interface::release_interface().

{
    if( readMeshIface )
    {
        mdbImpl->release_interface( readMeshIface );
        readMeshIface = 0;
    }
}

Member Function Documentation

ErrorCode ReadGmsh::create_elements	(	const GmshElemType &	type,
		const std::vector< int > &	elem_ids,
		const std::vector< int > &	matl_ids,
		const std::vector< int > &	geom_ids,
		const std::vector< int > &	prtn_ids,
		const std::vector< EntityHandle > &	connectivity,
		const Tag *	file_id_tag
	)		`[private]`

Create an element sequence.

Definition at line 325 of file ReadGmsh.cpp.

References create_sets(), ErrorCode, moab::ReadUtilIface::get_element_connect(), globalId, moab::Range::insert(), MB_START_ID, MB_SUCCESS, moab::GmshElemType::mb_type, MBVERTEX, mdbImpl, moab::GmshElemType::node_order, moab::GmshElemType::num_nodes, readMeshIface, moab::Interface::tag_set_data(), and moab::ReadUtilIface::update_adjacencies().

Referenced by load_file().

{
    ErrorCode result;

    // Make sure input is consistent
    const unsigned long num_elem = elem_ids.size();
    const int node_per_elem      = type.num_nodes;
    if( matl_ids.size() != num_elem || geom_ids.size() != num_elem || prtn_ids.size() != num_elem ||
        connectivity.size() != num_elem * node_per_elem )
        return MB_FAILURE;

    // Create the element sequence
    // for points, simply gather the connectivities and create the materials
    if( type.mb_type == MBVERTEX )
    {
        Range elements;
        elements.insert< std::vector< EntityHandle > >( connectivity.begin(), connectivity.end() );
        result = create_sets( type.mb_type, elements, matl_ids, 0 );
        if( MB_SUCCESS != result ) return result;

        return MB_SUCCESS;
    }
    EntityHandle handle = 0;
    EntityHandle* conn_array;
    result =
        readMeshIface->get_element_connect( num_elem, node_per_elem, type.mb_type, MB_START_ID, handle, conn_array );
    if( MB_SUCCESS != result ) return result;

    // Copy passed element connectivity into entity sequence data.
    if( type.node_order )
    {
        for( unsigned long i = 0; i < num_elem; ++i )
            for( int j = 0; j < node_per_elem; ++j )
                conn_array[i * node_per_elem + type.node_order[j]] = connectivity[i * node_per_elem + j];
    }
    else
    {
        memcpy( conn_array, &connectivity[0], connectivity.size() * sizeof( EntityHandle ) );
    }

    // Notify MOAB of the new elements
    result = readMeshIface->update_adjacencies( handle, num_elem, node_per_elem, conn_array );
    if( MB_SUCCESS != result ) return result;

    // Store element IDs
    Range elements( handle, handle + num_elem - 1 );
    result = mdbImpl->tag_set_data( globalId, elements, &elem_ids[0] );
    if( MB_SUCCESS != result ) return result;
    if( file_id_tag )
    {
        result = mdbImpl->tag_set_data( *file_id_tag, elements, &elem_ids[0] );
        if( MB_SUCCESS != result ) return result;
    }

    // Add elements to material sets
    result = create_sets( type.mb_type, elements, matl_ids, 0 );
    if( MB_SUCCESS != result ) return result;
    // Add elements to geometric sets
    result = create_sets( type.mb_type, elements, geom_ids, 1 );
    if( MB_SUCCESS != result ) return result;
    // Add elements to parallel partitions
    result = create_sets( type.mb_type, elements, prtn_ids, 2 );
    if( MB_SUCCESS != result ) return result;

    return MB_SUCCESS;
}

ErrorCode ReadGmsh::create_geometric_topology ( ) [private]

NOT IMPLEMENTED Reconstruct parent-child relations for geometry sets from mesh connectivity.

Definition at line 516 of file ReadGmsh.cpp.

References moab::Range::clear(), moab::Range::empty(), geomSets, and MB_SUCCESS.

Referenced by load_file().

{
    if( geomSets.empty() ) return MB_SUCCESS;

    // Not implemented yet
    geomSets.clear();
    return MB_SUCCESS;
}

ErrorCode ReadGmsh::create_sets	(	EntityType	element_type,
		const Range &	elements,
		const std::vector< int > &	set_ids,
		int	set_type
	)		`[private]`

Add elements to sets as dictated by grouping ID in file.

Definition at line 399 of file ReadGmsh.cpp.

References moab::Interface::add_entities(), moab::Range::begin(), moab::Interface::create_meshset(), dim, moab::CN::Dimension(), moab::Range::empty(), moab::Range::end(), entities, ErrorCode, GEOM_DIMENSION_TAG_NAME, geomSets, moab::Interface::get_entities_by_type_and_tag(), globalId, moab::Range::insert(), moab::intersect(), MATERIAL_SET_TAG_NAME, MB_ENTITY_NOT_FOUND, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TYPE_INTEGER, MBENTITYSET, mdbImpl, MESHSET_SET, PARALLEL_PARTITION_TAG_NAME, moab::Interface::tag_get_data(), moab::Interface::tag_get_handle(), and moab::Interface::tag_set_data().

Referenced by create_elements().

{
    ErrorCode result;

    // Get a unique list of set IDs
    std::set< int > ids;
    for( std::vector< int >::const_iterator i = set_ids.begin(); i != set_ids.end(); ++i )
        ids.insert( *i );

    // No Sets?
    if( ids.empty() || ( ids.size() == 1 && *ids.begin() == 0 ) ) return MB_SUCCESS;  // no sets (all ids are zero)

    // Get/create tag handles
    int num_tags;
    Tag tag_handles[2];
    int tag_val;
    const void* tag_values[2] = { &tag_val, NULL };

    switch( set_type )
    {
        default:
            return MB_FAILURE;
        case 0:
        case 2: {
            const char* name = set_type ? PARALLEL_PARTITION_TAG_NAME : MATERIAL_SET_TAG_NAME;
            result = mdbImpl->tag_get_handle( name, 1, MB_TYPE_INTEGER, tag_handles[0], MB_TAG_SPARSE | MB_TAG_CREAT );
            if( MB_SUCCESS != result ) return result;
            num_tags = 1;
            break;
        }
        case 1: {
            result = mdbImpl->tag_get_handle( GEOM_DIMENSION_TAG_NAME, 1, MB_TYPE_INTEGER, tag_handles[1],
                                              MB_TAG_SPARSE | MB_TAG_CREAT );
            if( MB_SUCCESS != result ) return result;
            tag_values[1]  = NULL;
            tag_handles[0] = globalId;
            num_tags       = 2;
            break;
        }
    }  // switch

    // For each unique set ID...
    for( std::set< int >::iterator i = ids.begin(); i != ids.end(); ++i )
    {
        // Skip "null" set ID
        if( *i == 0 ) continue;

        // Get all entities with the current set ID
        Range entities, sets;
        std::vector< int >::const_iterator j = set_ids.begin();
        for( Range::iterator k = elements.begin(); k != elements.end(); ++j, ++k )
            if( *i == *j ) entities.insert( *k );

        // Get set by ID
        // Cppcheck warning (false positive): variable tag_val is assigned a value that is never
        // used
        tag_val = *i;
        result  = mdbImpl->get_entities_by_type_and_tag( 0, MBENTITYSET, tag_handles, tag_values, num_tags, sets );
        if( MB_SUCCESS != result && MB_ENTITY_NOT_FOUND != result ) return result;

        // Don't use existing geometry sets (from some other file)
        if( 1 == set_type )  // Geometry
            sets = intersect( sets, geomSets );

        // Get set handle
        EntityHandle set;
        // If no sets with ID, create one
        if( sets.empty() )
        {
            result = mdbImpl->create_meshset( MESHSET_SET, set );
            if( MB_SUCCESS != result ) return result;

            result = mdbImpl->tag_set_data( tag_handles[0], &set, 1, &*i );
            if( MB_SUCCESS != result ) return result;

            if( 1 == set_type )
            {  // Geometry
                int dim = CN::Dimension( type );
                result  = mdbImpl->tag_set_data( tag_handles[1], &set, 1, &dim );
                if( MB_SUCCESS != result ) return result;
                geomSets.insert( set );
            }
        }
        else
        {
            set = *sets.begin();
            if( 1 == set_type )
            {  // Geometry
                int dim = CN::Dimension( type );
                // Get dimension of set
                int dim2;
                result = mdbImpl->tag_get_data( tag_handles[1], &set, 1, &dim2 );
                if( MB_SUCCESS != result ) return result;
                // If we're putting geometry of a higher dimension into the
                // set, increase the dimension of the set.
                if( dim > dim2 )
                {
                    result = mdbImpl->tag_set_data( tag_handles[1], &set, 1, &dim );
                    if( MB_SUCCESS != result ) return result;
                }
            }
        }

        // Put the mesh entities into the set
        result = mdbImpl->add_entities( set, entities );
        if( MB_SUCCESS != result ) return result;
    }  // for (ids)

    return MB_SUCCESS;
}

ReaderIface * ReadGmsh::factory ( Interface * iface ) [static]

factory method

Definition at line 44 of file ReadGmsh.cpp.

References ReadGmsh().

Referenced by moab::ReaderWriterSet::ReaderWriterSet().

{
    return new ReadGmsh( iface );
}

ErrorCode ReadGmsh::load_file	(	const char *	file_name,
		const EntityHandle *	file_set,
		const FileOptions &	opts,
		const SubsetList *	subset_list = `0`,
		const Tag *	file_id_tag = `0`
	)		`[virtual]`

Load mesh from a file.

Method all readers must provide to import a mesh.

Parameters:

file_name	The file to read.
file_set	Optional pointer to entity set representing file. If this is not NULL, reader may optionally tag the pointed-to set with format-specific meta-data.
subset_list	An optional struct pointer specifying the tags identifying entity sets to be read.
file_id_tag	If specified, reader should store for each entity it reads, a unique integer ID for this tag.

Author:: Jason Kraftcheck

Implements moab::ReaderIface.

Definition at line 72 of file ReadGmsh.cpp.

References moab::Range::clear(), create_elements(), create_geometric_topology(), ErrorCode, geomSets, moab::FileTokenizer::get_doubles(), moab::FileTokenizer::get_integers(), moab::FileTokenizer::get_long_ints(), moab::FileTokenizer::get_newline(), moab::ReadUtilIface::get_node_coords(), moab::FileTokenizer::get_string(), globalId, moab::Interface::globalId_tag(), moab::GmshUtil::gmshElemTypes, moab::FileTokenizer::line_number(), moab::FileTokenizer::match_token(), MATERIAL_SET_TAG_NAME, MB_FILE_DOES_NOT_EXIST, MB_FILE_WRITE_ERROR, MB_SET_ERR, MB_START_ID, MB_SUCCESS, MB_UNSUPPORTED_OPERATION, MBMAXTYPE, mdbImpl, moab::GmshElemType::num_nodes, moab::ReaderIface::IDTag::num_tag_values, moab::GmshUtil::numGmshElemType, readMeshIface, moab::ReaderIface::SubsetList::tag_list, moab::ReaderIface::SubsetList::tag_list_length, moab::ReaderIface::IDTag::tag_name, moab::Interface::tag_set_data(), and moab::ReaderIface::IDTag::tag_values.

{
    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, "GMsh 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;
    }

    geomSets.clear();
    globalId = mdbImpl->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;
    int data_size = 8;

    // Open file and hand off pointer to tokenizer
    FILE* file_ptr = fopen( filename, "r" );
    if( !file_ptr )
    {
        MB_SET_ERR( MB_FILE_DOES_NOT_EXIST, filename << ": " << strerror( errno ) );
    }
    FileTokenizer tokens( file_ptr, readMeshIface );

    // Determine file format version
    const char* const start_tokens[] = { "$NOD", "$MeshFormat", 0 };
    int format_version               = tokens.match_token( start_tokens );
    if( !format_version ) return MB_FILE_DOES_NOT_EXIST;

    // If version 2.0, read additional header info
    if( 2 == format_version )
    {
        double version;
        if( !tokens.get_doubles( 1, &version ) ) return MB_FILE_WRITE_ERROR;

        if( version != 2.0 && version != 2.1 && version != 2.2 )
        {
            MB_SET_ERR( MB_FILE_DOES_NOT_EXIST, filename << ": unknown format version: " << version );
            return MB_FILE_DOES_NOT_EXIST;
        }

        int file_format;
        if( !tokens.get_integers( 1, &file_format ) || !tokens.get_integers( 1, &data_size ) ||
            !tokens.match_token( "$EndMeshFormat" ) )
            return MB_FILE_WRITE_ERROR;
        // If physical entities in the gmsh file -> discard this
        const char* const phys_tokens[] = { "$Nodes", "$PhysicalNames", 0 };
        int hasPhys                     = tokens.match_token( phys_tokens );

        if( hasPhys == 2 )
        {
            long num_phys;
            if( !tokens.get_long_ints( 1, &num_phys ) ) return MB_FILE_WRITE_ERROR;
            for( long loop_phys = 0; loop_phys < num_phys; loop_phys++ )
            {
                long physDim;
                long physGroupNum;
                // char const * physName;
                if( !tokens.get_long_ints( 1, &physDim ) ) return MB_FILE_WRITE_ERROR;
                if( !tokens.get_long_ints( 1, &physGroupNum ) ) return MB_FILE_WRITE_ERROR;
                const char* ptc = tokens.get_string();
                if( !ptc ) return MB_FILE_WRITE_ERROR;
                // try to get to the end of the line, without reporting errors
                // really, we need to skip this
                while( !tokens.get_newline( false ) )
                    ptc = tokens.get_string();
            }
            if( !tokens.match_token( "$EndPhysicalNames" ) || !tokens.match_token( "$Nodes" ) )
                return MB_FILE_WRITE_ERROR;
        }
    }

    // Read number of nodes
    long num_nodes;
    if( !tokens.get_long_ints( 1, &num_nodes ) ) return MB_FILE_WRITE_ERROR;

    // Allocate nodes
    std::vector< double* > coord_arrays;
    EntityHandle handle = 0;
    ErrorCode result    = readMeshIface->get_node_coords( 3, num_nodes, MB_START_ID, handle, coord_arrays );
    if( MB_SUCCESS != result ) return result;

    // Read nodes
    double *x = coord_arrays[0], *y = coord_arrays[1], *z = coord_arrays[2];
    for( long i = 0; i < num_nodes; ++i, ++handle )
    {
        long id;
        if( !tokens.get_long_ints( 1, &id ) || !tokens.get_doubles( 1, x++ ) || !tokens.get_doubles( 1, y++ ) ||
            !tokens.get_doubles( 1, z++ ) )
            return MB_FILE_WRITE_ERROR;

        if( !node_id_map.insert( std::pair< long, EntityHandle >( id, handle ) ).second )
        {
            MB_SET_ERR( MB_FILE_WRITE_ERROR, "Duplicate node ID at line " << tokens.line_number() );
        }
    }

    // Create reverse map from handle to id
    std::vector< int > ids( num_nodes );
    std::vector< int >::iterator id_iter = ids.begin();
    std::vector< EntityHandle > handles( num_nodes );
    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 = mdbImpl->tag_set_data( globalId, &handles[0], num_nodes, &ids[0] );
    if( MB_SUCCESS != result ) return result;
    if( file_id_tag )
    {
        result = mdbImpl->tag_set_data( *file_id_tag, &handles[0], num_nodes, &ids[0] );
        if( MB_SUCCESS != result ) return result;
    }
    ids.clear();
    handles.clear();

    // Get tokens signifying end of node data and start of elements
    if( !tokens.match_token( format_version == 1 ? "$ENDNOD" : "$EndNodes" ) ||
        !tokens.match_token( format_version == 1 ? "$ELM" : "$Elements" ) )
        return MB_FILE_WRITE_ERROR;

    // Get element count
    long num_elem;
    if( !tokens.get_long_ints( 1, &num_elem ) ) return MB_FILE_WRITE_ERROR;

    // Lists of data accumulated for elements
    std::vector< EntityHandle > connectivity;
    std::vector< int > mat_set_list, geom_set_list, part_set_list, id_list;
    // Temporary, per-element data
    std::vector< int > int_data( 5 ), tag_data( 2 );
    std::vector< long > tmp_conn;
    int curr_elem_type = -1;
    for( long i = 0; i < num_elem; ++i )
    {
        // Read element description
        // File format 1.0
        if( 1 == format_version )
        {
            if( !tokens.get_integers( 5, &int_data[0] ) ) return MB_FILE_WRITE_ERROR;
            tag_data[0] = int_data[2];
            tag_data[1] = int_data[3];
            if( (unsigned)tag_data[1] < GmshUtil::numGmshElemType &&
                GmshUtil::gmshElemTypes[tag_data[1]].num_nodes != (unsigned)int_data[4] )
            {
                MB_SET_ERR( MB_FILE_WRITE_ERROR,
                            "Invalid node count for element type at line " << tokens.line_number() );
            }
        }
        // File format 2.0
        else
        {
            if( !tokens.get_integers( 3, &int_data[0] ) ) return MB_FILE_WRITE_ERROR;
            tag_data.resize( int_data[2] );
            if( !tokens.get_integers( tag_data.size(), &tag_data[0] ) ) return MB_FILE_WRITE_ERROR;
        }

        // If a list of material sets was specified in the
        // argument list, skip any elements for which the
        // material set is not specified or is not in the
        // passed list.
        if( !blocks.empty() && ( tag_data.empty() || blocks.find( tag_data[0] ) != blocks.end() ) ) continue;

        // If the next element is not the same type as the last one,
        // create a sequence for the block of elements we've read
        // to this point (all of the same type), and clear accumulated
        // data.
        if( int_data[1] != curr_elem_type )
        {
            if( !id_list.empty() )
            {  // First iteration
                result = create_elements( GmshUtil::gmshElemTypes[curr_elem_type], id_list, mat_set_list, geom_set_list,
                                          part_set_list, connectivity, file_id_tag );
                if( MB_SUCCESS != result ) return result;
            }

            id_list.clear();
            mat_set_list.clear();
            geom_set_list.clear();
            part_set_list.clear();
            connectivity.clear();
            curr_elem_type = int_data[1];
            if( (unsigned)curr_elem_type >= GmshUtil::numGmshElemType ||
                GmshUtil::gmshElemTypes[curr_elem_type].mb_type == MBMAXTYPE )
            {
                MB_SET_ERR( MB_FILE_WRITE_ERROR,
                            "Unsupported element type " << curr_elem_type << " at line " << tokens.line_number() );
            }
            tmp_conn.resize( GmshUtil::gmshElemTypes[curr_elem_type].num_nodes );
        }

        // Store data from element description
        id_list.push_back( int_data[0] );
        if( tag_data.size() > 3 )
            part_set_list.push_back( tag_data[3] );  // it must be new format for gmsh, >= 2.5
                                                     // it could have negative partition ids, for ghost elements
        else if( tag_data.size() > 2 )
            part_set_list.push_back( tag_data[2] );  // old format, partition id saved in 3rd tag field
        else
            part_set_list.push_back( 0 );
        geom_set_list.push_back( tag_data.size() > 1 ? tag_data[1] : 0 );
        mat_set_list.push_back( tag_data.size() > 0 ? tag_data[0] : 0 );

        // Get element connectivity
        if( !tokens.get_long_ints( tmp_conn.size(), &tmp_conn[0] ) ) return MB_FILE_WRITE_ERROR;

        // Convert connectivity from IDs to handles
        for( unsigned j = 0; j < tmp_conn.size(); ++j )
        {
            std::map< long, EntityHandle >::iterator k = node_id_map.find( tmp_conn[j] );
            if( k == node_id_map.end() )
            {
                MB_SET_ERR( MB_FILE_WRITE_ERROR, "Invalid node ID at line " << tokens.line_number() );
            }
            connectivity.push_back( k->second );
        }
    }  // for (num_nodes)

    // Create entity sequence for last element(s).
    if( !id_list.empty() )
    {
        result = create_elements( GmshUtil::gmshElemTypes[curr_elem_type], id_list, mat_set_list, geom_set_list,
                                  part_set_list, connectivity, file_id_tag );
        if( MB_SUCCESS != result ) return result;
    }

    // Construct parent-child relations for geometric sets.
    // Note:  At the time this comment was written, the following
    //        function was not implemented.
    result = create_geometric_topology();
    geomSets.clear();
    return result;
}

ErrorCode ReadGmsh::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`
	)		`[virtual]`

Read tag values from a file.

Read the list if all integer tag values from the file for a tag that is a single integer value per entity.

Parameters:

file_name	The file to read.
tag_name	The tag for which to read values
tag_values_out	Output: The list of tag values.
subset_list	An array of tag name and value sets specifying the subset of the file to read. If multiple tags are specified, the sets that match all tags (intersection) should be read.
subset_list_length	The length of the 'subset_list' array.