1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
/**
 * 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;<--- Assignment 'material_set_list=0', assigned value is 0<--- Assignment 'material_set_list=0', assigned value is 0

    if( subset_list )<--- Assuming condition is false<--- Assuming condition is false
    {
        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;<--- Null pointer addition
         ++material_set_list )<--- Null pointer addition
        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