ReadGmsh.cpp

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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.
 *
 */
 
/**
 * \class ReadGmsh
 * \brief Gmsh (http://www.geuz.org/gmsh) file reader
 *
 * See: http://geuz.org/gmsh/doc/texinfo/gmsh.html#MSH-ASCII-file-format
 *
 * \author Jason Kraftcheck
 */
 
#include "ReadGmsh.hpp"
#include "FileTokenizer.hpp"  // for file tokenizer
#include "Internals.hpp"
#include "moab/Interface.hpp"
#include "moab/ReadUtilIface.hpp"
#include "moab/Range.hpp"
#include "MBTagConventions.hpp"
#include "MBParallelConventions.h"
#include "moab/CN.hpp"
#include "GmshUtil.hpp"
 
#include <cerrno>
#include <cstring>
#include <map>
#include <set>
 
namespace moab
{
 
ReaderIface* ReadGmsh::factory( Interface* iface )
{
    return new ReadGmsh( iface );
}
 
ReadGmsh::ReadGmsh( Interface* impl ) : mdbImpl( impl ), globalId( 0 )
{
    mdbImpl->query_interface( readMeshIface );
}
 
ReadGmsh::~ReadGmsh()
{
    if( readMeshIface )
    {
        mdbImpl->release_interface( readMeshIface );
        readMeshIface = 0;
    }
}
 
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 */ )
{
    return MB_NOT_IMPLEMENTED;
}
 
ErrorCode ReadGmsh::load_file( const char* filename,
                               const EntityHandle*,
                               const FileOptions&,
                               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, "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;
}
 
//! Create an element sequence
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 )
{
    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;
}
 
//! Add elements to sets as dictated by grouping ID in file.
ErrorCode ReadGmsh::create_sets( EntityType type,
                                 const Range& elements,
                                 const std::vector< int >& set_ids,
                                 int set_type )
{
    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;
}
 
//! NOT IMPLEMENTED
//! Reconstruct parent-child relations for geometry sets from
//! mesh connectivity.
ErrorCode ReadGmsh::create_geometric_topology()
{
    if( geomSets.empty() ) return MB_SUCCESS;
 
    // Not implemented yet
    geomSets.clear();
    return MB_SUCCESS;
}
 
}  // namespace moab