Mesh Oriented datABase  (version 5.5.1)
An array-based unstructured mesh library
DirectAccessWithHoles.cpp
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1 /** @example DirectAccessWithHoles.cpp \n
2  * \brief Use direct access to MOAB data to avoid calling through API \n
3  *
4  * This example creates a 1d row of quad elements, with a user-specified number of "holes" (missing
5  * quads) in the row: \verbatim
6  * ---------------------- ---------------------- --------
7  * | | | | | | | | | |
8  * | | | |(hole)| | | |(hole)| | ...
9  * | | | | | | | | | |
10  * ---------------------- ---------------------- --------
11  * \endverbatim
12  * This makes (nholes+1) contiguous runs of quad handles in the handle space
13  * This example shows how to use the xxx_iterate functions in MOAB (xxx = coords, connect, tag,
14  * adjacencies) to get direct pointer access to MOAB internal storage, which can be used without
15  * calling through the MOAB API.
16  *
17  * -# Initialize MOAB \n
18  * -# Create a quad mesh with holes, as depicted above
19  * -# Create 2 dense tags (tag1, tag2) for avg position to assign to quads, and # verts per quad
20  * (tag3)
21  * -# Get connectivity, coordinate, tag1 iterators
22  * -# Iterate through quads, computing midpoint based on vertex positions, set on quad-based
23  * tag1
24  * -# Set up map from starting quad handle for a chunk to struct of (tag1_ptr, tag2_ptr,
25  * tag3_ptr), pointers to the dense tag storage for those tags for the chunk
26  * -# Iterate through vertices, summing positions into tag2 on connected quads and incrementing
27  * vertex count
28  * -# Iterate through quads, normalizing tag2 by vertex count and comparing values of tag1 and
29  * tag2
30  *
31  * <b>To compile</b>: \n
32  * make DirectAccessWithHoles \n
33  * <b>To run</b>: ./DirectAccess [-nquads <# quads>] [-holes <# holes>]\n
34  *
35  */
36 
37 #include "moab/Core.hpp"
38 #include "moab/ProgOptions.hpp"
39 #include "moab/ReadUtilIface.hpp"
40 #include <map>
41 #include <iostream>
42 #include <cassert>
43 
44 using namespace moab;
45 using namespace std;
46 
47 ErrorCode create_mesh_with_holes( Interface* mbImpl, int nquads, int nholes );
48 
49 struct tag_struct
50 {
51  double* avg_ptr;
52  int* nv_ptr;
53 };
54 
55 int main( int argc, char** argv )
56 {
57  // Get MOAB instance
58  Interface* mbImpl = new( std::nothrow ) Core;
59  if( NULL == mbImpl ) return 1;
60 
61  int nquads = 1000, nholes = 1;
62 
63  // Parse options
64  ProgOptions opts;
65  opts.addOpt< int >( string( "nquads,n" ), string( "Number of quads in the mesh (default = 1000" ), &nquads );
66  opts.addOpt< int >( string( "holes,H" ), string( "Number of holes in the element handle space (default = 1" ),
67  &nholes );
68  opts.parseCommandLine( argc, argv );
69  if( nholes >= nquads )
70  {
71  cerr << "Number of holes needs to be < number of elements." << endl;
72  return 1;
73  }
74 
75  // Create simple structured mesh with hole, but using unstructured representation
76  ErrorCode rval = create_mesh_with_holes( mbImpl, nquads, nholes );MB_CHK_SET_ERR( rval, "Trouble creating mesh" );
77 
78  // Get all vertices and non-vertex entities
79  Range verts, elems;
80  rval = mbImpl->get_entities_by_handle( 0, elems );MB_CHK_SET_ERR( rval, "Trouble getting all entities" );
81  verts = elems.subset_by_dimension( 0 );
82  elems -= verts;
83 
84  // Create tag1 (element-based avg), tag2 (vertex-based avg), tag3 (# connected verts)
85  Tag tag1, tag2, tag3;
86  rval = mbImpl->tag_get_handle( "tag1", 3, MB_TYPE_DOUBLE, tag1, MB_TAG_DENSE | MB_TAG_CREAT );MB_CHK_SET_ERR( rval, "Trouble creating tag1" );
87  double def_val[3] = { 0.0, 0.0, 0.0 }; // Need a default value for tag2 because we sum into it
88  rval = mbImpl->tag_get_handle( "tag2", 3, MB_TYPE_DOUBLE, tag2, MB_TAG_DENSE | MB_TAG_CREAT, def_val );MB_CHK_SET_ERR( rval, "Trouble creating tag2" );
89  int def_val_int = 0; // Need a default value for tag3 because we increment it
90  rval = mbImpl->tag_get_handle( "tag3", 1, MB_TYPE_INTEGER, tag3, MB_TAG_DENSE | MB_TAG_CREAT, &def_val_int );MB_CHK_SET_ERR( rval, "Trouble creating tag3" );
91 
92  // Get connectivity, coordinate, tag, and adjacency iterators
93  EntityHandle* conn_ptr;
94  double *x_ptr, *y_ptr, *z_ptr, *tag1_ptr, *tag2_ptr;
95  int* tag3_ptr;
96 
97  // First vertex is at start of range (ranges are sorted), and is offset for vertex index
98  // calculation
99  EntityHandle first_vert = *verts.begin();
100 
101  // When iterating over elements, each chunk can have a different # vertices; also, count tells
102  // you how many elements are in the current chunk
103  int vpere, count;
104 
105  // Get coordinates iterator, just need this once because we know verts handle space doesn't have
106  // holes
107  rval = mbImpl->coords_iterate( verts.begin(), verts.end(), x_ptr, y_ptr, z_ptr, count );MB_CHK_SET_ERR( rval, "Error in coords_iterate" );
108  assert( count == (int)verts.size() ); // Should end up with just one contiguous chunk of vertices
109 
110  // Iterate through elements, computing midpoint based on vertex positions, set on element-based
111  // tag1 Control loop by iterator over elem range
112  Range::iterator e_it = elems.begin();
113 
114  while( e_it != elems.end() )
115  {
116  // Get conn_ptr, tag1_ptr for next contiguous chunk of element handles, and coords pointers
117  // for all verts
118  rval = mbImpl->connect_iterate( e_it, elems.end(), conn_ptr, vpere, count );MB_CHK_SET_ERR( rval, "Error in connect_iterate" );
119  rval = mbImpl->tag_iterate( tag1, e_it, elems.end(), count, (void*&)tag1_ptr );MB_CHK_SET_ERR( rval, "Error in tag1_iterate" );
120 
121  // Iterate over elements in this chunk
122  for( int i = 0; i < count; i++ )
123  {
124  tag1_ptr[0] = tag1_ptr[1] = tag1_ptr[2] = 0.0; // Initialize position for this element
125  for( int j = 0; j < vpere; j++ )
126  { // Loop over vertices in this element
127  int v_index = conn_ptr[j] - first_vert; // vert index is just the offset from first vertex
128  tag1_ptr[0] += x_ptr[v_index];
129  tag1_ptr[1] += y_ptr[v_index]; // Sum vertex positions into tag1...
130  tag1_ptr[2] += z_ptr[v_index];
131  }
132  tag1_ptr[0] /= vpere;
133  tag1_ptr[1] /= vpere; // Then normalize
134  tag1_ptr[2] /= vpere;
135 
136  // Done with this element; advance connect_ptr and tag1_ptr to next element
137  conn_ptr += vpere;
138  tag1_ptr += 3;
139  } // Loop over elements in chunk
140 
141  // Done with chunk; advance range iterator by count; will skip over gaps in range
142  e_it += count;
143  } // While loop over all elements
144 
145  // Iterate through vertices, summing positions into tag2 on connected elements and incrementing
146  // vertex count Iterate over chunks the same as elements, even though we know we have only one
147  // chunk here, just to show how it's done
148 
149  // Create a std::map from EntityHandle (first entity handle in chunk) to
150  // tag_struct (ptrs to start of avg/#verts tags for that chunk); then for a given entity handle,
151  // we can quickly find the chunk it's in using map::lower_bound; could have set up this map in
152  // earlier loop over elements, but do it here for clarity
153 
154  map< EntityHandle, tag_struct > elem_map;
155  e_it = elems.begin();
156  while( e_it != elems.end() )
157  {
158  tag_struct ts = { NULL, NULL };
159  rval = mbImpl->tag_iterate( tag2, e_it, elems.end(), count, (void*&)ts.avg_ptr );MB_CHK_SET_ERR( rval, "Error in tag2_iterate" );
160  rval = mbImpl->tag_iterate( tag3, e_it, elems.end(), count, (void*&)ts.nv_ptr );MB_CHK_SET_ERR( rval, "Error in tag3_iterate" );
161  elem_map[*e_it] = ts;
162  e_it += count;
163  }
164 
165  // Call a vertex-quad adjacencies function to generate vertex-element adjacencies in MOAB
166  Range::iterator v_it = verts.begin();
167  Range dum_range;
168  rval = mbImpl->get_adjacencies( &( *v_it ), 1, 2, false, dum_range );MB_CHK_SET_ERR( rval, "Error in get_adjacencies" );
169  const vector< EntityHandle >** adjs_ptr;
170  while( v_it != verts.end() )
171  {
172  // Get coords ptrs, adjs_ptr; can't set tag2_ptr by direct access, because of hole in
173  // element handle space
174  rval = mbImpl->coords_iterate( v_it, verts.end(), x_ptr, y_ptr, z_ptr, count );MB_CHK_SET_ERR( rval, "Error in coords_iterate" );
175  rval = mbImpl->adjacencies_iterate( v_it, verts.end(), adjs_ptr, count );MB_CHK_SET_ERR( rval, "Error in adjacencies_iterate" );
176 
177  for( int v = 0; v < count; v++ )
178  {
179  const vector< EntityHandle >* avec = *( adjs_ptr + v );
180  for( vector< EntityHandle >::const_iterator ait = avec->begin(); ait != avec->end(); ++ait )
181  {
182  // Get chunk that this element resides in; upper_bound points to the first element
183  // strictly > key, so get that and decrement (would work the same as lower_bound
184  // with an if-test and decrement)
185  map< EntityHandle, tag_struct >::iterator mit = elem_map.upper_bound( *ait );
186  --mit;
187  // Index of *ait in that chunk
188  int a_ind = *ait - ( *mit ).first;
189  tag_struct ts = ( *mit ).second;
190  ts.avg_ptr[3 * a_ind + 0] += x_ptr[v]; // Tag on each element is 3 doubles, x/y/z
191  ts.avg_ptr[3 * a_ind + 1] += y_ptr[v];
192  ts.avg_ptr[3 * a_ind + 2] += z_ptr[v];
193  ts.nv_ptr[a_ind]++; // Increment the vertex count
194  }
195  }
196 
197  v_it += count;
198  }
199 
200  // Normalize tag2 by vertex count; loop over elements using same approach as before
201  // At the same time, compare values of tag1 and tag2
202  e_it = elems.begin();
203  while( e_it != elems.end() )
204  {
205  // Get conn_ptr, tag1_ptr for next contiguous chunk of element handles, and coords pointers
206  // for all verts
207  rval = mbImpl->tag_iterate( tag1, e_it, elems.end(), count, (void*&)tag1_ptr );MB_CHK_SET_ERR( rval, "Error in tag1_iterate" );
208  rval = mbImpl->tag_iterate( tag2, e_it, elems.end(), count, (void*&)tag2_ptr );MB_CHK_SET_ERR( rval, "Error in tag2_iterate" );
209  rval = mbImpl->tag_iterate( tag3, e_it, elems.end(), count, (void*&)tag3_ptr );MB_CHK_SET_ERR( rval, "Error in tag3_iterate" );
210 
211  // Iterate over elements in this chunk
212  for( int i = 0; i < count; i++ )
213  {
214  for( int j = 0; j < 3; j++ )
215  tag2_ptr[3 * i + j] /= (double)tag3_ptr[i]; // Normalize by # verts
216  if( tag1_ptr[3 * i] != tag2_ptr[3 * i] || tag1_ptr[3 * i + 1] != tag2_ptr[3 * i + 1] ||
217  tag1_ptr[3 * i + 2] != tag2_ptr[3 * i + 2] )
218  cout << "Tag1, tag2 disagree for element " << *e_it + i << endl;
219  }
220 
221  e_it += count;
222  }
223 
224  // Ok, we're done, shut down MOAB
225  delete mbImpl;
226 
227  return 0;
228 }
229 
230 ErrorCode create_mesh_with_holes( Interface* mbImpl, int nquads, int nholes )
231 {
232  // First make the mesh, a 1d array of quads with left hand side x = elem_num; vertices are
233  // numbered in layers
234  ReadUtilIface* read_iface;
235  ErrorCode rval = mbImpl->query_interface( read_iface );MB_CHK_SET_ERR( rval, "Error in query_interface" );
236  vector< double* > coords;
237  EntityHandle start_vert, start_elem, *connect;
238  // Create verts, num is 4(nquads+1) because they're in a 1d row; will initialize coords in loop
239  // over elems later
240  rval = read_iface->get_node_coords( 3, 2 * ( nquads + 1 ), 0, start_vert, coords );MB_CHK_SET_ERR( rval, "Error in get_node_arrays" );
241  // Create elems
242  rval = read_iface->get_element_connect( nquads, 4, MBQUAD, 0, start_elem, connect );MB_CHK_SET_ERR( rval, "Error in get_element_connect" );
243  for( int i = 0; i < nquads; i++ )
244  {
245  coords[0][2 * i] = coords[0][2 * i + 1] = (double)i; // x values are all i
246  coords[1][2 * i] = 0.0;
247  coords[1][2 * i + 1] = 1.0; // y coords
248  coords[2][2 * i] = coords[2][2 * i + 1] = (double)0.0; // z values, all zero (2d mesh)
249  EntityHandle quad_v = start_vert + 2 * i;
250  for( int j = 0; j < 4; j++ )
251  connect[4 * i + j] = quad_v + j; // Connectivity of each quad is a sequence starting from quad_v
252  }
253  // Last two vertices
254  // Cppcheck warning (false positive): variable coords is assigned a value that is never used
255  coords[0][2 * nquads] = coords[0][2 * nquads + 1] = (double)nquads;
256  coords[1][2 * nquads] = 0.0;
257  coords[1][2 * nquads + 1] = 1.0; // y coords
258  coords[2][2 * nquads] = coords[2][2 * nquads + 1] = (double)0.0; // z values, all zero (2d mesh)
259 
260  // Now delete nholes elements, spaced approximately equally through mesh, so contiguous size is
261  // about nquads/(nholes + 1) reinterpret start_elem as the next element to be deleted
262  int de = nquads / ( nholes + 1 );
263  for( int i = 0; i < nholes; i++ )
264  {
265  start_elem += de;
266  rval = mbImpl->delete_entities( &start_elem, 1 );MB_CHK_SET_ERR( rval, "Error in delete_entities" );
267  }
268 
269  return MB_SUCCESS;
270 }