Line data Source code
1 : // The libMesh Finite Element Library.
2 : // Copyright (C) 2002-2025 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
3 :
4 : // This library is free software; you can redistribute it and/or
5 : // modify it under the terms of the GNU Lesser General Public
6 : // License as published by the Free Software Foundation; either
7 : // version 2.1 of the License, or (at your option) any later version.
8 :
9 : // This library is distributed in the hope that it will be useful,
10 : // but WITHOUT ANY WARRANTY; without even the implied warranty of
11 : // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
12 : // Lesser General Public License for more details.
13 :
14 : // You should have received a copy of the GNU Lesser General Public
15 : // License along with this library; if not, write to the Free Software
16 : // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
17 :
18 : #ifndef LIBMESH_EXODUSII_IO_HELPER_H
19 : #define LIBMESH_EXODUSII_IO_HELPER_H
20 :
21 : #include "libmesh/libmesh_config.h"
22 :
23 : #ifdef LIBMESH_HAVE_EXODUS_API
24 :
25 : // Local includes
26 : #include "libmesh/parallel_object.h"
27 : #include "libmesh/point.h"
28 : #include "libmesh/boundary_info.h" // BoundaryInfo::BCTuple
29 : #include "libmesh/enum_elem_type.h" // INVALID_ELEM
30 : #include "libmesh/exodus_header_info.h"
31 :
32 : // C++ includes
33 : #include <iostream>
34 : #include <string>
35 : #include <vector>
36 : #include <map>
37 :
38 : // Macros to simplify checking Exodus error codes
39 : #define EX_CHECK_ERR(code, msg) \
40 : do { \
41 : if ((code) < 0) { \
42 : libmesh_error_msg((msg)); \
43 : } } while (0)
44 :
45 : #define EX_EXCEPTIONLESS_CHECK_ERR(code, msg) \
46 : do { \
47 : if ((code) < 0) { \
48 : libMesh::err << (msg) << std::endl; \
49 : libmesh_exceptionless_error(); \
50 : } } while (0)
51 :
52 : // Before we include a header wrapped in a namespace, we'd better make
53 : // sure none of its dependencies end up in that namespace
54 : #include <errno.h>
55 : #include <stddef.h>
56 : #include <stdlib.h>
57 : #include <stdint.h>
58 :
59 : namespace libMesh
60 : {
61 :
62 : // Forward declarations
63 : class MeshBase;
64 : class DofObject;
65 :
66 : /**
67 : * This is the \p ExodusII_IO_Helper class. This class hides the
68 : * implementation details of interfacing with the Exodus binary
69 : * format.
70 : *
71 : * \author John W. Peterson
72 : * \date 2002
73 : */
74 8668 : class ExodusII_IO_Helper : public ParallelObject
75 : {
76 : public:
77 : /**
78 : * Constructor. Automatically initializes all the private members of
79 : * the class. Also allows you to set the verbosity level to v=true
80 : * (on) or v=false (off). The second argument, if true, tells the class to only
81 : * perform its actions if running on processor zero. If you initialize this
82 : * to false, the writing methods will run on all processors instead.
83 : */
84 : ExodusII_IO_Helper(const ParallelObject & parent,
85 : bool v=false,
86 : bool run_only_on_proc0=true,
87 : bool single_precision=false);
88 : /**
89 : * Special functions. This class does not manage any dynamically
90 : * allocated resources (file pointers, etc.) so it _should_ be
91 : * default copy/move constructable, but I don't know
92 : * if any existing code actually uses these operations.
93 : */
94 : ExodusII_IO_Helper (const ExodusII_IO_Helper &) = default;
95 : ExodusII_IO_Helper (ExodusII_IO_Helper &&) = default;
96 : virtual ~ExodusII_IO_Helper();
97 :
98 : /**
99 : * This class contains references so it can't be default
100 : * copy/move-assigned.
101 : */
102 : ExodusII_IO_Helper & operator= (const ExodusII_IO_Helper &) = delete;
103 : ExodusII_IO_Helper & operator= (ExodusII_IO_Helper &&) = delete;
104 :
105 : /**
106 : * \returns The ExodusII API version, in "nodot" format; e.g. 822
107 : * for 8.22
108 : */
109 : static int get_exodus_version();
110 :
111 : /**
112 : * \returns The current element type.
113 : *
114 : * \note The default behavior is for this value to be in all capital
115 : * letters, e.g. \p HEX27.
116 : */
117 : const char * get_elem_type() const;
118 :
119 : /**
120 : * Sets whether or not to write extra "side" elements. This is useful for
121 : * plotting SIDE_DISCONTINUOUS data.
122 : */
123 : void set_add_sides(bool add_sides);
124 :
125 : bool get_add_sides();
126 :
127 : /**
128 : * Opens an \p ExodusII mesh file named \p filename. If
129 : * read_only==true, the file will be opened with the EX_READ flag,
130 : * otherwise it will be opened with the EX_WRITE flag.
131 : */
132 : void open(const char * filename, bool read_only);
133 :
134 : /**
135 : * Reads an \p ExodusII mesh file header, leaving this object's
136 : * internal data structures unchanged.
137 : */
138 : ExodusHeaderInfo read_header() const;
139 :
140 : /**
141 : * Reads an \p ExodusII mesh file header, and stores required
142 : * information on this object.
143 : */
144 : void read_and_store_header_info();
145 :
146 : /**
147 : * Reads the QA records from an ExodusII file. We can use this to
148 : * detect when e.g. CUBIT 14+ was used to generate a Mesh file, and
149 : * work around certain known bugs in that version.
150 : */
151 : void read_qa_records();
152 :
153 : /**
154 : * Prints the \p ExodusII mesh file header, which includes the mesh
155 : * title, the number of nodes, number of elements, mesh dimension,
156 : * number of sidesets, and number of nodesets.
157 : */
158 : void print_header();
159 :
160 : /**
161 : * Reads the nodal data (x,y,z coordinates) from the \p ExodusII
162 : * mesh file.
163 : */
164 : void read_nodes();
165 :
166 : /**
167 : * Reads the optional \p node_num_map from the \p ExodusII mesh
168 : * file.
169 : */
170 : void read_node_num_map();
171 :
172 : /**
173 : * Reads the optional \p bex_cv_blocks from the \p ExodusII mesh
174 : * file.
175 : */
176 : void read_bex_cv_blocks();
177 :
178 : /**
179 : * Prints the nodal information, by default to \p libMesh::out.
180 : */
181 : void print_nodes(std::ostream & out_stream = libMesh::out);
182 :
183 : /**
184 : * Reads information for all of the blocks in the \p ExodusII mesh
185 : * file.
186 : */
187 : void read_block_info();
188 :
189 : /**
190 : * Get the block number for the given block index.
191 : */
192 : int get_block_id(int index);
193 :
194 : /**
195 : * Get the block name for the given block index if supplied in
196 : * the mesh file. Otherwise an empty string is returned.
197 : */
198 : std::string get_block_name(int index);
199 :
200 : /**
201 : * Get the side set id for the given side set index.
202 : */
203 : int get_side_set_id(int index);
204 :
205 : /**
206 : * Get the side set name for the given side set index if supplied in
207 : * the mesh file. Otherwise an empty string is returned.
208 : */
209 : std::string get_side_set_name(int index);
210 :
211 : /**
212 : * Get the node set id for the given node set index.
213 : */
214 : int get_node_set_id(int index);
215 :
216 : /**
217 : * Get the node set name for the given node set index if supplied in
218 : * the mesh file. Otherwise an empty string is returned.
219 : */
220 : std::string get_node_set_name(int index);
221 :
222 : /**
223 : * Reads all of the element connectivity for block \p block in the
224 : * \p ExodusII mesh file.
225 : */
226 : void read_elem_in_block(int block);
227 :
228 : /**
229 : * Read in edge blocks, storing information in the BoundaryInfo object.
230 : */
231 : void read_edge_blocks(MeshBase & mesh);
232 :
233 : /**
234 : * Reads the optional \p node_num_map from the \p ExodusII mesh
235 : * file.
236 : */
237 : void read_elem_num_map();
238 :
239 : /**
240 : * Reads information about all of the sidesets in the \p ExodusII
241 : * mesh file.
242 : */
243 : void read_sideset_info();
244 :
245 : /**
246 : * Reads information about all of the nodesets in the \p ExodusII
247 : * mesh file.
248 : */
249 : void read_nodeset_info();
250 :
251 : /**
252 : * Reads information about all of the elemsets in the \p ExodusII
253 : * mesh file.
254 : */
255 : void read_elemset_info();
256 :
257 : /**
258 : * Reads information about sideset \p id and inserts it into the
259 : * global sideset array at the position \p offset.
260 : */
261 : void read_sideset(int id, int offset);
262 :
263 : /**
264 : * Reads information about elemset \p id and inserts it into the
265 : * global elemset array at the position \p offset.
266 : */
267 : void read_elemset(int id, int offset);
268 :
269 : /**
270 : * New API that reads all nodesets simultaneously. This may be slightly
271 : * faster than reading them one at a time. Calls ex_get_concat_node_sets()
272 : * under the hood.
273 : */
274 : void read_all_nodesets();
275 :
276 : /**
277 : * Closes the \p ExodusII mesh file.
278 : *
279 : * This function is called from the ExodusII_IO destructor, so it should
280 : * not throw an exception.
281 : */
282 : void close() noexcept;
283 :
284 : /**
285 : * Reads and stores the timesteps in the 'time_steps' array.
286 : */
287 : void read_time_steps();
288 :
289 : /**
290 : * Reads the number of timesteps currently stored in the Exodus file
291 : * and stores it in the num_time_steps variable.
292 : */
293 : void read_num_time_steps();
294 :
295 : /**
296 : * Reads the nodal values for the variable 'nodal_var_name' at the
297 : * specified time into the 'nodal_var_values' array.
298 : */
299 : void read_nodal_var_values(std::string nodal_var_name, int time_step);
300 :
301 : /**
302 : * Reads elemental values for the variable 'elemental_var_name' at the
303 : * specified timestep into the 'elem_var_value_map' which is passed in.
304 : */
305 : void read_elemental_var_values(std::string elemental_var_name,
306 : int time_step,
307 : std::map<dof_id_type, Real> & elem_var_value_map);
308 :
309 : /**
310 : * Helper function that takes a (1-based) Exodus node/elem id and
311 : * determines the corresponding libMesh Node/Elem id. Takes into account
312 : * whether the user has chosen to set the Node/Elem unique ids based on
313 : * the {node,elem}_num_map or to let libMesh set them.
314 : */
315 : dof_id_type get_libmesh_node_id(int exodus_node_id);
316 : dof_id_type get_libmesh_elem_id(int exodus_elem_id);
317 :
318 : /**
319 : * Helper function that conditionally sets the unique_id of the
320 : * passed-in Node/Elem. Calling this function does nothing if
321 : * _set_unique_ids_from_maps == false, otherwise it sets the
322 : * unique_id based on the entries of the {node,elem_num_map}. The
323 : * input index is assumed to be a zero-based index into the
324 : * {node,elem}_num_map array.
325 : */
326 : void conditionally_set_node_unique_id(
327 : MeshBase & mesh, Node * node, int zero_based_node_num_map_index);
328 : void conditionally_set_elem_unique_id(
329 : MeshBase & mesh, Elem * elem, int zero_based_elem_num_map_index);
330 :
331 : private:
332 :
333 : /**
334 : * Internal implementation for the two sets of functions above.
335 : */
336 : dof_id_type get_libmesh_id(
337 : int exodus_id,
338 : const std::vector<int> & num_map);
339 :
340 : void set_dof_object_unique_id(
341 : MeshBase & mesh,
342 : DofObject * dof_object,
343 : int exodus_mapped_id);
344 :
345 : public:
346 :
347 : /**
348 : * Opens an \p ExodusII mesh file named \p filename for writing.
349 : */
350 : virtual void create(std::string filename);
351 :
352 : /**
353 : * Initializes the Exodus file.
354 : */
355 : virtual void initialize(std::string title, const MeshBase & mesh, bool use_discontinuous=false);
356 :
357 : /**
358 : * Writes the nodal coordinates contained in "mesh"
359 : */
360 : virtual void write_nodal_coordinates(const MeshBase & mesh, bool use_discontinuous=false);
361 :
362 : /**
363 : * Writes the elements contained in "mesh". FIXME: This only works
364 : * for Meshes having a single type of element in each subdomain!
365 : *
366 : * If \p use_discontinuous is true, we break apart elements, so that
367 : * shared nodes on faces/edges/vertices can take different values
368 : * from different elements. This is useful for plotting
369 : * discontinuous underlying variables
370 : *
371 : * If \p _add_sides is true, we also output side elements, so that
372 : * shared nodes on edges/vertices can take different values from
373 : * different elements. This is useful for plotting
374 : * SIDE_DISCONTINUOUS representing e.g. inter-element fluxes.
375 : */
376 : virtual void write_elements(const MeshBase & mesh,
377 : bool use_discontinuous=false);
378 :
379 : /**
380 : * Writes the sidesets contained in "mesh"
381 : */
382 : virtual void write_sidesets(const MeshBase & mesh);
383 :
384 : /**
385 : * Writes the nodesets contained in "mesh"
386 : */
387 : virtual void write_nodesets(const MeshBase & mesh);
388 :
389 : /**
390 : * Sets up the nodal variables
391 : */
392 : virtual void initialize_element_variables(std::vector<std::string> names,
393 : const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains);
394 :
395 : /**
396 : * Sets up the nodal variables
397 : */
398 : void initialize_nodal_variables(std::vector<std::string> names);
399 :
400 : /**
401 : * Sets up the global variables
402 : */
403 : void initialize_global_variables(std::vector<std::string> names);
404 :
405 : /**
406 : * Writes the time for the timestep
407 : */
408 : void write_timestep(int timestep, Real time);
409 :
410 : /**
411 : * Write elemsets stored on the Mesh to the exo file.
412 : */
413 : void write_elemsets(const MeshBase & mesh);
414 :
415 : /**
416 : * Write sideset data for the requested timestep.
417 : */
418 : void
419 : write_sideset_data (const MeshBase & mesh,
420 : int timestep,
421 : const std::vector<std::string> & var_names,
422 : const std::vector<std::set<boundary_id_type>> & side_ids,
423 : const std::vector<std::map<BoundaryInfo::BCTuple, Real>> & bc_vals);
424 :
425 : /**
426 : * Read sideset variables, if any, into the provided data structures.
427 : */
428 : void
429 : read_sideset_data (const MeshBase & mesh,
430 : int timestep,
431 : std::vector<std::string> & var_names,
432 : std::vector<std::set<boundary_id_type>> & side_ids,
433 : std::vector<std::map<BoundaryInfo::BCTuple, Real>> & bc_vals);
434 :
435 : /**
436 : * Similar to read_sideset_data(), but instead of creating one
437 : * std::map per sideset per variable, creates a single map of (elem,
438 : * side, boundary_id) tuples, and stores the exo file array indexing
439 : * for any/all sideset variables on that sideset (they are all the
440 : * same). This function does not actually call exII::ex_get_sset_var()
441 : * to get values, and can be useful if only the original ordering of
442 : * (elem, side) pairs in the exo file is required in cases where a
443 : * separate approach is used to read the sideset data arrays.
444 : */
445 : void
446 : get_sideset_data_indices (const MeshBase & mesh,
447 : std::map<BoundaryInfo::BCTuple, unsigned int> & bc_array_indices);
448 :
449 : /**
450 : * Write nodeset data for the requested timestep.
451 : */
452 : void
453 : write_nodeset_data (int timestep,
454 : const std::vector<std::string> & var_names,
455 : const std::vector<std::set<boundary_id_type>> & node_boundary_ids,
456 : const std::vector<std::map<BoundaryInfo::NodeBCTuple, Real>> & bc_vals);
457 :
458 : /**
459 : * Read nodeset variables, if any, into the provided data structures.
460 : */
461 : void
462 : read_nodeset_data (int timestep,
463 : std::vector<std::string> & var_names,
464 : std::vector<std::set<boundary_id_type>> & node_boundary_ids,
465 : std::vector<std::map<BoundaryInfo::NodeBCTuple, Real>> & bc_vals);
466 :
467 : /**
468 : * Similar to read_nodeset_data(), but instead of creating one
469 : * std::map per nodeset per variable, creates a single map of
470 : * (node_id, boundary_id) tuples, and stores the exo file array
471 : * indexing for any/all nodeset variables on that nodeset (they are
472 : * all the same).
473 : */
474 : void
475 : get_nodeset_data_indices (std::map<BoundaryInfo::NodeBCTuple, unsigned int> & bc_array_indices);
476 :
477 : /**
478 : * Write elemset data for the requested timestep.
479 : */
480 : void
481 : write_elemset_data (int timestep,
482 : const std::vector<std::string> & var_names,
483 : const std::vector<std::set<elemset_id_type>> & elemset_ids_in,
484 : const std::vector<std::map<std::pair<dof_id_type, elemset_id_type>, Real>> & elemset_vals);
485 :
486 : /**
487 : * Read elemset variables, if any, into the provided data structures.
488 : */
489 : void
490 : read_elemset_data (int timestep,
491 : std::vector<std::string> & var_names,
492 : std::vector<std::set<elemset_id_type>> & elemset_ids_in,
493 : std::vector<std::map<std::pair<dof_id_type, elemset_id_type>, Real>> & elemset_vals);
494 :
495 : /**
496 : * Similar to read_elemset_data(), but instead of creating one
497 : * std::map per elemset per variable, creates a single map of
498 : * (elem_id, elemset_id) tuples, and stores the exo file array
499 : * indexing for any/all elemset variables on that elemset (they are
500 : * all the same).
501 : */
502 : void
503 : get_elemset_data_indices (std::map<std::pair<dof_id_type, elemset_id_type>, unsigned int> & elemset_array_indices);
504 :
505 : /**
506 : * Writes the vector of values to the element variables.
507 : *
508 : * The 'values' vector is assumed to be in the order:
509 : * {(u1, u2, u3, ..., uN), (v1, v2, v3, ..., vN), (w1, w2, w3, ..., wN)}
510 : * where N is the number of elements.
511 : *
512 : * This ordering is produced by calls to ES::build_elemental_solution_vector().
513 : * ES::build_discontinuous_solution_vector(), on the other hand, produces an
514 : * element-major ordering. See the function below for that case.
515 : */
516 : void write_element_values
517 : (const MeshBase & mesh,
518 : const std::vector<Real> & values,
519 : int timestep,
520 : const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains);
521 :
522 : /**
523 : * Same as the function above, but assume the input 'values' vector is
524 : * in element-major order, i.e.
525 : * {(u1,v1,w1), (u2,v2,w2), ... (uN,vN,wN)}
526 : * This function is called by
527 : * ExodusII_IO::write_element_data_from_discontinuous_nodal_data()
528 : * because ES::build_discontinuous_solution_vector() builds the solution
529 : * vector in this order.
530 : *
531 : * \note If some variables are subdomain-restricted, then the tuples will
532 : * be of different lengths for each element, i.e.
533 : * {(u1,v1,w1), (u2,v2), ... (uN,vN,wN)}
534 : * if variable w is not active on element 2.
535 : */
536 : void write_element_values_element_major
537 : (const MeshBase & mesh,
538 : const std::vector<Real> & values,
539 : int timestep,
540 : const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains,
541 : const std::vector<std::string> & derived_var_names,
542 : const std::map<subdomain_id_type, std::vector<std::string>> & subdomain_to_var_names);
543 :
544 : /**
545 : * Writes the vector of values to a nodal variable.
546 : */
547 : void write_nodal_values(int var_id, const std::vector<Real> & values, int timestep);
548 :
549 : /**
550 : * Writes the vector of information records.
551 : */
552 : void write_information_records(const std::vector<std::string> & records);
553 :
554 : /**
555 : * Writes the vector of global variables.
556 : */
557 : void write_global_values(const std::vector<Real> & values, int timestep);
558 :
559 : /**
560 : * Uses ex_update() to flush buffers to file.
561 : */
562 : void update();
563 :
564 : /**
565 : * Reads the vector of global variables.
566 : */
567 : void read_global_values(std::vector<Real> & values, int timestep);
568 :
569 : /**
570 : * Sets the underlying value of the boolean flag
571 : * _use_mesh_dimension_instead_of_spatial_dimension. By default,
572 : * the value of this flag is false.
573 : *
574 : * See the ExodusII_IO class documentation for a detailed
575 : * description of this flag.
576 : */
577 : void use_mesh_dimension_instead_of_spatial_dimension(bool val);
578 :
579 : /**
580 : * Set to true (the default) to write files in an HDF5-based file
581 : * format (when HDF5 is available), or to false to write files in
582 : * the old NetCDF3-based format. If HDF5 is unavailable, this
583 : * setting does nothing.
584 : */
585 : void set_hdf5_writing(bool write_hdf5);
586 :
587 : /**
588 : * Sets the value of _write_as_dimension.
589 : *
590 : * This directly controls the num_dim which is written to the Exodus
591 : * file. If non-zero, this value supersedes all other dimensions,
592 : * including:
593 : * 1.) MeshBase::spatial_dimension()
594 : * 2.) MeshBase::mesh_dimension()
595 : * 3.) Any value passed to use_mesh_dimension_instead_of_spatial_dimension()
596 : * This is useful/necessary for working around a bug in Paraview which
597 : * prevents the "Plot Over Line" filter from working on 1D meshes.
598 : */
599 : void write_as_dimension(unsigned dim);
600 :
601 : /**
602 : * Allows you to set a vector that is added to the coordinates of all
603 : * of the nodes. Effectively, this "moves" the mesh to a particular position
604 : */
605 : void set_coordinate_offset(Point p);
606 :
607 : /**
608 : * \returns A vector with three copies of each element in the provided name vector,
609 : * starting with r_, i_ and a_ respectively. If the "write_complex_abs" parameter
610 : * is true (default), the complex modulus is written, otherwise only the real and
611 : * imaginary parts are written.
612 : */
613 : std::vector<std::string>
614 : get_complex_names(const std::vector<std::string> & names,
615 : bool write_complex_abs) const;
616 :
617 : /**
618 : * returns a "tripled" copy of \p vars_active_subdomains, which is necessary in the
619 : * complex-valued case.
620 : */
621 : std::vector<std::set<subdomain_id_type>>
622 : get_complex_vars_active_subdomains
623 : (const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains,
624 : bool write_complex_abs) const;
625 :
626 : /**
627 : * Takes a map from subdomain id -> vector of active variable names
628 : * as input and returns a corresponding map where the original
629 : * variable names have been replaced by their complex counterparts.
630 : * Used by the ExodusII_IO::write_element_data_from_discontinuous_nodal_data()
631 : * function.
632 : */
633 : std::map<subdomain_id_type, std::vector<std::string>>
634 : get_complex_subdomain_to_var_names
635 : (const std::map<subdomain_id_type, std::vector<std::string>> & subdomain_to_var_names,
636 : bool write_complex_abs) const;
637 :
638 : /**
639 : * This is the \p ExodusII_IO_Helper Conversion class. It provides
640 : * a data structure which contains \p ExodusII node/edge maps and
641 : * name conversions. It's defined below.
642 : */
643 : class Conversion;
644 :
645 : /**
646 : * This is the \p ExodusII_IO_Helper NamesData class.
647 : * It manages the C data structure necessary for writing out named
648 : * entities to ExodusII files.
649 : */
650 : class NamesData;
651 :
652 : /**
653 : * Prints the message defined in \p msg. Can be turned off if
654 : * verbosity is set to 0.
655 : */
656 : void message(std::string_view msg);
657 :
658 : /**
659 : * Prints the message defined in \p msg, and appends the number \p i
660 : * to the end of the message. Useful for printing messages in
661 : * loops. Can be turned off if verbosity is set to 0.
662 : */
663 : void message(std::string_view msg, int i);
664 :
665 : // File identification flag
666 : int ex_id;
667 :
668 : // General error flag
669 : int ex_err;
670 :
671 : // struct which contains data fields from the Exodus file header
672 : ExodusHeaderInfo header_info;
673 :
674 : // Problem title (Use vector<char> to emulate a char *)
675 : std::vector<char> & title;
676 :
677 : // Number of dimensions in the mesh
678 : int & num_dim;
679 :
680 : // Total number of nodes in the mesh
681 : int & num_nodes;
682 :
683 : // Total number of elements in the mesh
684 : int & num_elem;
685 :
686 : // Smallest element id which exceeds every element id in the mesh.
687 : // (this may exceed num_elem due to mapping)
688 : int end_elem_id() const;
689 :
690 : // Total number of element blocks
691 : int & num_elem_blk;
692 :
693 : // Total number of edges
694 : int & num_edge;
695 :
696 : // Total number of edge blocks. The sum of the number of edges in
697 : // each block must equal num_edge.
698 : int & num_edge_blk;
699 :
700 : // Total number of node sets
701 : int & num_node_sets;
702 :
703 : // Total number of side sets
704 : int & num_side_sets;
705 :
706 : // Total number of element sets
707 : int & num_elem_sets;
708 :
709 : // Number of global variables
710 : int num_global_vars;
711 :
712 : // Number of sideset variables
713 : int num_sideset_vars;
714 :
715 : // Number of nodeset variables
716 : int num_nodeset_vars;
717 :
718 : // Number of elemset variables
719 : int num_elemset_vars;
720 :
721 : // Number of elements in this block
722 : int num_elem_this_blk;
723 :
724 : // Number of nodes in each element
725 : int num_nodes_per_elem;
726 :
727 : // Number of attributes for a given block
728 : int num_attr;
729 :
730 : // Total number of elements in all side sets
731 : int num_elem_all_sidesets;
732 :
733 : // Total number of elements in all elem sets
734 : int num_elem_all_elemsets;
735 :
736 : // Vector of element block identification numbers
737 : std::vector<int> block_ids;
738 :
739 : // Vector of edge block identification numbers
740 : std::vector<int> edge_block_ids;
741 :
742 : // Vector of nodes in an element
743 : std::vector<int> connect;
744 :
745 : // Vector of the sideset IDs
746 : std::vector<int> ss_ids;
747 :
748 : // Vector of the nodeset IDs
749 : std::vector<int> nodeset_ids;
750 :
751 : // Vector of the elemset IDs
752 : std::vector<int> elemset_ids;
753 :
754 : // Number of sides in each sideset
755 : std::vector<int> num_sides_per_set;
756 :
757 : // Number of nodes in each nodeset
758 : std::vector<int> num_nodes_per_set;
759 :
760 : // Number of elems in each elemset
761 : std::vector<int> num_elems_per_set;
762 :
763 : // Number of distribution factors per sideset
764 : std::vector<int> num_df_per_set;
765 :
766 : // Number of distribution factors per nodeset
767 : std::vector<int> num_node_df_per_set;
768 :
769 : // Number of distribution factors per elemset
770 : std::vector<int> num_elem_df_per_set;
771 :
772 : // Starting indices for each nodeset in the node_sets_node_list vector.
773 : // Used in the calls to ex_{put,get}_concat_node_sets().
774 : std::vector<int> node_sets_node_index;
775 :
776 : // Starting indices for each nodeset in the node_sets_dist_fact vector.
777 : // Used in the calls to ex_{put,get}_concat_node_sets().
778 : std::vector<int> node_sets_dist_index;
779 :
780 : // Node ids for all nodes in nodesets, concatenated together.
781 : // Used in the calls to ex_{put,get}_concat_node_sets().
782 : std::vector<int> node_sets_node_list;
783 :
784 : // Distribution factors for all nodes in all nodesets, concatenated together.
785 : // Used in the calls to ex_{put,get}_concat_node_sets().
786 : std::vector<Real> node_sets_dist_fact;
787 :
788 : // List of element numbers in all sidesets
789 : std::vector<int> elem_list;
790 :
791 : // Side (face/edge) number actually on the boundary
792 : std::vector<int> side_list;
793 :
794 : // Side (face/edge) id number
795 : std::vector<int> id_list;
796 :
797 : // List of element numbers in all elemsets
798 : std::vector<int> elemset_list;
799 :
800 : // List of elemset ids for all elements in elemsets
801 : std::vector<int> elemset_id_list;
802 :
803 : // Optional mapping from internal [0,num_nodes) to arbitrary indices
804 : std::vector<int> node_num_map;
805 :
806 : // Optional mapping from internal [0,num_elem) to arbitrary indices
807 : std::vector<int> elem_num_map;
808 :
809 : // x locations of node points
810 : std::vector<Real> x;
811 :
812 : // y locations of node points
813 : std::vector<Real> y;
814 :
815 : // z locations of node points
816 : std::vector<Real> z;
817 :
818 : // Spline weights associated with node points, in IGA meshes
819 : std::vector<Real> w;
820 :
821 : // Number of Bezier Extraction coefficient vectors in a block
822 : unsigned int bex_num_elem_cvs;
823 :
824 : // Bezier Extraction connectivity indices, in IGA meshes
825 : std::vector<std::vector<long unsigned int>> bex_cv_conn;
826 :
827 : // Bezier Extraction coefficient vectors, in IGA meshes
828 : // bex_dense_constraint_vecs[block_num][vec_num][column_num] = coef
829 : std::vector<std::vector<std::vector<Real>>> bex_dense_constraint_vecs;
830 :
831 : // Type of element in a given block
832 : std::vector<char> elem_type;
833 :
834 : // Maps libMesh element numbers to Exodus element numbers
835 : // gets filled in when write_elements gets called
836 : std::map<dof_id_type, dof_id_type> libmesh_elem_num_to_exodus;
837 : std::vector<int> exodus_elem_num_to_libmesh;
838 :
839 : // Map of all node numbers connected to local node numbers to their exodus numbering.
840 : // The exodus numbers are stored in here starting with 1
841 : std::map<dof_id_type, dof_id_type> libmesh_node_num_to_exodus;
842 : std::vector<int> exodus_node_num_to_libmesh;
843 :
844 : // The number of timesteps in the file, as returned by ex_inquire
845 : int num_time_steps;
846 :
847 : // The timesteps stored in the solution file, filled by read_time_steps()
848 : std::vector<Real> time_steps;
849 :
850 : // The number of nodal variables in the Exodus file
851 : int num_nodal_vars;
852 :
853 : // The names of the nodal variables stored in the Exodus file
854 : std::vector<std::string> nodal_var_names;
855 :
856 : // Holds the nodal variable values for a given variable, one value
857 : // per node, indexed by libMesh node id.
858 : // This is a map so it can handle Nemesis files as well.
859 : std::map<dof_id_type, Real> nodal_var_values;
860 :
861 : // The number of elemental variables in the Exodus file
862 : int num_elem_vars;
863 :
864 : // The names of the elemental variables stored in the Exodus file
865 : std::vector<std::string> elem_var_names;
866 :
867 : // Holds the elemental variable values for a given variable, one value per element
868 : std::vector<Real> elem_var_values;
869 :
870 : // The names of the global variables stored in the Exodus file
871 : std::vector<std::string> global_var_names;
872 :
873 : // The names of the sideset variables stored in the Exodus file
874 : std::vector<std::string> sideset_var_names;
875 :
876 : // The names of the nodeset variables stored in the Exodus file
877 : std::vector<std::string> nodeset_var_names;
878 :
879 : // The names of the elemset variables stored in the Exodus file
880 : std::vector<std::string> elemset_var_names;
881 :
882 : // Maps of Ids to named entities
883 : std::map<int, std::string> id_to_block_names;
884 : std::map<int, std::string> id_to_edge_block_names;
885 : std::map<int, std::string> id_to_ss_names;
886 : std::map<int, std::string> id_to_ns_names;
887 : std::map<int, std::string> id_to_elemset_names;
888 :
889 : // On/Off message flag
890 : bool verbose;
891 :
892 : // Same as the ExodusII_IO flag by the same name. This flag is
893 : // also set whenever ExodusII_IO::set_unique_ids_from_maps() is called.
894 : bool set_unique_ids_from_maps;
895 :
896 : // This flag gets set after the Exodus file has been successfully opened for writing.
897 : // Both the create() and open() (if called with EX_WRITE) functions may set this flag.
898 : bool opened_for_writing;
899 :
900 : // This flag gets set after the open() function has been successfully called.
901 : // We call open() to open an ExodusII file for reading.
902 : bool opened_for_reading;
903 :
904 : // When either create() or open() is called, the Helper stores the
905 : // name of the opened file as current_filename. This way, the
906 : // ExodusII_IO object can check to see if, on subsequent writes, the
907 : // user is asking to write to a *different* filename from the one
908 : // that is currently open, and signal an error. The current
909 : // ExodusII_IO implementation is designed to work with a single file
910 : // only, so if you want to write to multiple Exodus files, use a
911 : // different ExodusII_IO object for each one.
912 : std::string current_filename;
913 :
914 : /**
915 : * Wraps calls to exII::ex_get_var_names() and exII::ex_get_var_param().
916 : * The enumeration controls whether nodal, elemental, global, etc.
917 : * variable names are read and which class members are filled in.
918 : * NODAL: num_nodal_vars nodal_var_names
919 : * ELEMENTAL: num_elem_vars elem_var_names
920 : * GLOBAL: num_global_vars global_var_names
921 : * SIDESET: num_sideset_vars sideset_var_names
922 : * NODESET: num_nodeset_vars nodeset_var_names
923 : */
924 : enum ExodusVarType {NODAL=0, ELEMENTAL=1, GLOBAL=2, SIDESET=3, NODESET=4, ELEMSET=5};
925 : void read_var_names(ExodusVarType type);
926 :
927 : const ExodusII_IO_Helper::Conversion &
928 : get_conversion(const ElemType type) const;
929 :
930 : const ExodusII_IO_Helper::Conversion &
931 : get_conversion(std::string type_str) const;
932 :
933 : /*
934 : * Returns the sum of node "offsets" that are to be expected from a
935 : * parallel nodal solution vector that has had "fake" nodes added on
936 : * each processor. This plus a node id gives a valid nodal solution
937 : * vector index.
938 : */
939 25337106 : dof_id_type node_id_to_vec_id(dof_id_type n) const
940 : {
941 25337106 : if (_added_side_node_offsets.empty())
942 23081537 : return n;
943 :
944 : // Find the processor id that has node_id in the parallel vec
945 12050 : const auto lb = std::upper_bound(_true_node_offsets.begin(),
946 2410 : _true_node_offsets.end(), n);
947 1205 : libmesh_assert(lb != _true_node_offsets.end());
948 14460 : const processor_id_type p = lb - _true_node_offsets.begin();
949 :
950 14460 : return n + (p ? _added_side_node_offsets[p-1] : 0);
951 : }
952 :
953 : /*
954 : * Returns the sum of both added node "offsets" on processors 0
955 : * through p-1 and real nodes added on processors 0 to p.
956 : * This is the starting index for added nodes' data.
957 : */
958 1725 : dof_id_type added_node_offset_on(processor_id_type p) const
959 : {
960 50 : libmesh_assert (p < _true_node_offsets.size());
961 : const dof_id_type added_node_offsets =
962 1800 : (_added_side_node_offsets.empty() || !p) ? 0 :
963 1475 : _added_side_node_offsets[p-1];
964 1825 : return _true_node_offsets[p] + added_node_offsets;
965 : }
966 :
967 :
968 : protected:
969 : /**
970 : * When appending: during initialization, check that variable names
971 : * in the file match those you attempt to initialize with.
972 : */
973 : void check_existing_vars(ExodusVarType type, std::vector<std::string> & names, std::vector<std::string> & names_from_file);
974 :
975 : /**
976 : * Wraps calls to exII::ex_put_var_names() and exII::ex_put_var_param().
977 : * The enumeration controls whether nodal, elemental, or global
978 : * variable names are read and which class members are filled in.
979 : */
980 : void write_var_names(ExodusVarType type, const std::vector<std::string> & names);
981 :
982 : // If true, whenever there is an I/O operation, only perform if if we are on processor 0.
983 : bool _run_only_on_proc0;
984 :
985 : // This flag gets set after the create() function has been successfully called.
986 : bool _opened_by_create;
987 :
988 : // True once the elem vars are initialized
989 : bool _elem_vars_initialized;
990 :
991 : // True once the global vars are initialized
992 : bool _global_vars_initialized;
993 :
994 : // True once the nodal vars are initialized
995 : bool _nodal_vars_initialized;
996 :
997 : // If true, use the Mesh's dimension (as determined by the dimension
998 : // of the elements comprising the mesh) instead of the mesh's
999 : // spatial dimension, when writing. By default this is false.
1000 : bool _use_mesh_dimension_instead_of_spatial_dimension;
1001 :
1002 : // If true, write an HDF5 file when available. If false, write the
1003 : // old format.
1004 : bool _write_hdf5;
1005 :
1006 : // Set once the elem num map has been read
1007 : int _end_elem_id;
1008 :
1009 : // Use this for num_dim when writing the Exodus file. If non-zero, supersedes
1010 : // any value set in _use_mesh_dimension_instead_of_spatial_dimension.
1011 : unsigned _write_as_dimension;
1012 :
1013 : // On output, shift every point by _coordinate_offset
1014 : Point _coordinate_offset;
1015 :
1016 : // If true, forces single precision I/O
1017 : bool _single_precision;
1018 :
1019 : /**
1020 : * If we're adding "fake" sides to visualize SIDE_DISCONTINUOUS
1021 : * variables, _added_side_node_offsets[p] gives us the total
1022 : * solution vector offset to use on processor p+1 from the nodes on
1023 : * those previous ranks' sides.
1024 : */
1025 : std::vector<dof_id_type> _added_side_node_offsets;
1026 :
1027 : /**
1028 : * If we're adding "fake" sides to visualize SIDE_DISCONTINUOUS
1029 : * variables, we also need to know how many real nodes from previous
1030 : * ranks are taking up space in a solution vector.
1031 : */
1032 : std::vector<dof_id_type> _true_node_offsets;
1033 :
1034 : /**
1035 : * This class facilitates inline conversion of an input data vector
1036 : * to a different precision level, depending on the underlying type
1037 : * of Real and whether or not the single_precision flag is set. This
1038 : * should be used whenever floating point data is being written to
1039 : * the Exodus file. Note that if no precision conversion has to take
1040 : * place, there should be very little overhead involved in using
1041 : * this object.
1042 : */
1043 : struct MappedOutputVector
1044 : {
1045 : // If necessary, allocates space to store a version of vec_in in a
1046 : // different precision than it was input with.
1047 : MappedOutputVector(const std::vector<Real> & vec_in,
1048 : bool single_precision_in);
1049 :
1050 45312 : ~MappedOutputVector() = default;
1051 :
1052 : // Returns void * pointer to either the mapped data or the
1053 : // original data, as necessary.
1054 : void * data();
1055 :
1056 : private:
1057 : const std::vector<Real> & our_data;
1058 : bool single_precision;
1059 : std::vector<double> double_vec;
1060 : std::vector<float> float_vec;
1061 : };
1062 :
1063 : /**
1064 : * This class facilitates reading in vectors from Exodus file that
1065 : * may be of a different floating point type than Real. It employs
1066 : * basically the same approach as the MappedOutputVector, just going
1067 : * in the opposite direction. For more information, see the
1068 : * MappedOutputVector class docs.
1069 : */
1070 : struct MappedInputVector
1071 : {
1072 : MappedInputVector(std::vector<Real> & vec_in,
1073 : bool single_precision_in);
1074 : ~MappedInputVector();
1075 :
1076 : // Returns void * pointer to either the mapped data or the
1077 : // original data, as necessary.
1078 : void * data();
1079 :
1080 : private:
1081 : std::vector<Real> & our_data;
1082 : bool single_precision;
1083 : std::vector<double> double_vec;
1084 : std::vector<float> float_vec;
1085 : };
1086 :
1087 :
1088 : protected:
1089 :
1090 : /**
1091 : * read_var_names() dispatches to this function. We need to
1092 : * override it slightly for Nemesis.
1093 : */
1094 : virtual void read_var_names_impl(const char * var_type,
1095 : int & count,
1096 : std::vector<std::string> & result);
1097 :
1098 : private:
1099 :
1100 : /**
1101 : * Set to true iff we want to write separate "side" elements too.
1102 : */
1103 : bool _add_sides = false;
1104 :
1105 : /**
1106 : * write_var_names() dispatches to this function.
1107 : */
1108 : void write_var_names_impl(const char * var_type,
1109 : int & count,
1110 : const std::vector<std::string> & names);
1111 :
1112 : /**
1113 : * Defines equivalence classes of Exodus element types that map to
1114 : * libmesh ElemTypes.
1115 : */
1116 : std::map<std::string, ElemType> element_equivalence_map;
1117 : void init_element_equivalence_map();
1118 :
1119 : /**
1120 : * Associates libMesh ElemTypes with node/face/edge/etc. mappings
1121 : * of the corresponding Exodus element types.
1122 : *
1123 : * We have to map based on both ElemType and mesh dimension, because
1124 : * Exodus treats "TRI" side numbering in two different ways
1125 : * depending on whether a triangle is embedded in a 2D or a 3D mesh.
1126 : */
1127 : std::map<int, std::map<ElemType, ExodusII_IO_Helper::Conversion>> conversion_map;
1128 : void init_conversion_map();
1129 : };
1130 :
1131 :
1132 :
1133 1789350 : class ExodusII_IO_Helper::Conversion
1134 : {
1135 : public:
1136 :
1137 : /**
1138 : * Constructor. Zero initializes all variables.
1139 : */
1140 1846650 : Conversion()
1141 1846650 : : node_map(nullptr),
1142 1789350 : inverse_node_map(nullptr),
1143 1789350 : side_map(nullptr),
1144 1789350 : inverse_side_map(nullptr),
1145 1789350 : shellface_map(nullptr),
1146 1789350 : inverse_shellface_map(nullptr),
1147 1789350 : shellface_index_offset(0),
1148 1789350 : libmesh_type(INVALID_ELEM),
1149 1789350 : dim(0),
1150 1789350 : n_nodes(0),
1151 1846650 : exodus_type("")
1152 1846650 : {}
1153 :
1154 : /**
1155 : * \returns The ith component of the node map for this element.
1156 : *
1157 : * The node map maps the exodusII node numbering format to this
1158 : * library's format.
1159 : */
1160 : int get_node_map(int i) const;
1161 :
1162 : /**
1163 : * \returns The ith component of the inverse node map for this
1164 : * element.
1165 : *
1166 : * The inverse node map maps the libmesh node numbering to Exodus'
1167 : * node numbering.
1168 : *
1169 : * \note All elements except Hex27 currently have the same node
1170 : * numbering as libmesh elements.
1171 : */
1172 : int get_inverse_node_map(int i) const;
1173 :
1174 : /**
1175 : * \returns The ith component of the side map for this element.
1176 : *
1177 : * The side map maps the exodusII side numbering format to this
1178 : * library's format.
1179 : */
1180 : int get_side_map(int i) const;
1181 :
1182 : /**
1183 : * \returns The ith component of the side map for this element.
1184 : *
1185 : * The side map maps the libMesh side numbering format to this
1186 : * exodus's format.
1187 : */
1188 : int get_inverse_side_map(int i) const;
1189 :
1190 : /**
1191 : * \returns The ith component of the shellface map for this element.
1192 : * \note Nothing is currently using this.
1193 : */
1194 : int get_shellface_map(int i) const;
1195 :
1196 : /**
1197 : * \returns The ith component of the inverse shellface map for this element.
1198 : */
1199 : int get_inverse_shellface_map(int i) const;
1200 :
1201 : /**
1202 : * \returns The canonical element type for this element.
1203 : *
1204 : * The canonical element type is the standard element type
1205 : * understood by this library.
1206 : */
1207 : ElemType libmesh_elem_type() const;
1208 :
1209 : /**
1210 : * \returns The string corresponding to the Exodus type for this element.
1211 : */
1212 : std::string exodus_elem_type() const;
1213 :
1214 : /**
1215 : * \returns The shellface index offset.
1216 : */
1217 : std::size_t get_shellface_index_offset() const;
1218 :
1219 : /**
1220 : * An invalid_id that can be returned to signal failure in case
1221 : * something goes wrong.
1222 : */
1223 : static const int invalid_id;
1224 :
1225 : /**
1226 : * Pointer to the node map for this element.
1227 : */
1228 : const std::vector<int> * node_map;
1229 :
1230 : /**
1231 : * Pointer to the inverse node map for this element.
1232 : * For all elements except for the Hex27, this is the same
1233 : * as the node map.
1234 : */
1235 : const std::vector<int> * inverse_node_map;
1236 :
1237 : /**
1238 : * Pointer to the side map for this element.
1239 : */
1240 : const std::vector<int> * side_map;
1241 :
1242 : /**
1243 : * Pointer to the inverse side map for this element.
1244 : */
1245 : const std::vector<int> * inverse_side_map;
1246 :
1247 : /**
1248 : * Pointer to the shellface map for this element. Only the inverse
1249 : * is actually used currently, this one is provided for completeness
1250 : * and libmesh_ingore()d to avoid warnings.
1251 : */
1252 : const std::vector<int> * shellface_map;
1253 :
1254 : /**
1255 : * Pointer to the inverse shellface map for this element.
1256 : */
1257 : const std::vector<int> * inverse_shellface_map;
1258 :
1259 : /**
1260 : * The shellface index offset defines the offset due to a difference between libMesh
1261 : * and Exodus in indexing sidesets. This is relevant for shell elements, for
1262 : * example, since Exodus includes extra "shell face" sides in that case.
1263 : */
1264 : size_t shellface_index_offset;
1265 :
1266 : /**
1267 : * The canonical (i.e. standard for this library)
1268 : * element type.
1269 : */
1270 : ElemType libmesh_type;
1271 :
1272 : /**
1273 : * The element dimension; useful since we don't seem to have a cheap
1274 : * way to look this up from ElemType
1275 : */
1276 : int dim;
1277 :
1278 : /**
1279 : * The number of nodes per element; useful likewise
1280 : */
1281 : int n_nodes;
1282 :
1283 : /**
1284 : * The string corresponding to the Exodus type for this element
1285 : */
1286 : std::string exodus_type;
1287 : };
1288 :
1289 :
1290 :
1291 : /**
1292 : * This class is useful for managing anything that requires a char **
1293 : * input/output in ExodusII file. You must know the number of strings
1294 : * and the length of each one at the time you create it.
1295 : */
1296 41914 : class ExodusII_IO_Helper::NamesData
1297 : {
1298 : public:
1299 : /**
1300 : * Constructor. Allocates enough storage to hold n_strings of
1301 : * length string_length. (Actually allocates string_length+1 characters
1302 : * per string to account for the trailing '\0' character.)
1303 : */
1304 : explicit
1305 : NamesData(size_t n_strings, size_t string_length);
1306 :
1307 : /**
1308 : * Adds another name to the current data table.
1309 : */
1310 : void push_back_entry(const std::string & name);
1311 :
1312 : /**
1313 : * Provide access to the underlying C data table
1314 : */
1315 : char ** get_char_star_star();
1316 :
1317 : /**
1318 : * Provide access to the i'th underlying char *
1319 : */
1320 : char * get_char_star(int i);
1321 :
1322 : private:
1323 : // C++ data structures for managing string memory
1324 : std::vector<std::vector<char>> data_table;
1325 : std::vector<char *> data_table_pointers;
1326 :
1327 : size_t counter;
1328 : size_t table_size;
1329 : };
1330 :
1331 :
1332 68 : inline void ExodusII_IO_Helper::set_add_sides(bool add_sides)
1333 : {
1334 2414 : _add_sides = add_sides;
1335 68 : }
1336 :
1337 :
1338 2751 : inline bool ExodusII_IO_Helper::get_add_sides()
1339 : {
1340 14420 : return _add_sides;
1341 : }
1342 :
1343 :
1344 0 : inline int ExodusII_IO_Helper::end_elem_id() const
1345 : {
1346 0 : libmesh_assert_equal_to(std::size_t(num_elem), elem_num_map.size());
1347 357 : return _end_elem_id;
1348 : }
1349 :
1350 :
1351 : } // namespace libMesh
1352 :
1353 : #endif // LIBMESH_HAVE_EXODUS_API
1354 :
1355 : #endif // LIBMESH_EXODUSII_IO_HELPER_H
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