/usr/include/dolfin/mesh/MeshValueCollection.h is in libdolfin1.3-dev 1.3.0+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 | // Copyright (C) 2011-2013 Anders Logg and Garth N. Wells
//
// This file is part of DOLFIN.
//
// DOLFIN 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 3 of the License, or
// (at your option) any later version.
//
// DOLFIN is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
//
// Modified by Chris Richardson, 2013.
//
// First added: 2006-08-30
// Last changed: 2013-05-22
#ifndef __MESH_VALUE_COLLECTION_H
#define __MESH_VALUE_COLLECTION_H
#include <map>
#include <utility>
#include <boost/shared_ptr.hpp>
#include <dolfin/common/NoDeleter.h>
#include <dolfin/common/Variable.h>
#include <dolfin/log/log.h>
#include "Cell.h"
#include "Mesh.h"
#include "MeshEntity.h"
#include "MeshFunction.h"
namespace dolfin
{
/// The MeshValueCollection class can be used to store data
/// associated with a subset of the entities of a mesh of a given
/// topological dimension. It differs from the MeshFunction class in
/// two ways. First, data does not need to be associated with all
/// entities (only a subset). Second, data is associated with
/// entities through the corresponding cell index and local entity
/// number (relative to the cell), not by global entity index, which
/// means that data may be stored robustly to file.
template <typename T>
class MeshValueCollection : public Variable
{
public:
/// Create empty mesh value collection
///
MeshValueCollection();
/// Create an empty mesh value collection on a given mesh
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh.
explicit MeshValueCollection(boost::shared_ptr<const Mesh> mesh);
/// Create a mesh value collection from a MeshFunction
///
/// *Arguments*
/// mesh_function (_MeshFunction_ <T>)
/// The mesh function for creating a MeshValueCollection.
explicit MeshValueCollection(const MeshFunction<T>& mesh_function);
/// Create a mesh value collection of entities of given dimension
/// on a given mesh
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh associated with the collection.
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
MeshValueCollection(const Mesh& mesh, std::size_t dim);
/// Create a mesh value collection of entities of given dimension
/// on a given mesh (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh associated with the collection.
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
MeshValueCollection(boost::shared_ptr<const Mesh> mesh, std::size_t dim);
/// Create a mesh value collection from a file.
///
/// *Arguments*
/// mesh (Mesh)
/// A mesh associated with the collection. The mesh is used to
/// map collection values to the appropriate process.
/// filename (std::string)
/// The XML file name.
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
MeshValueCollection(const Mesh& mesh, const std::string filename);
/// Destructor
~MeshValueCollection() {}
/// Assignment operator
///
/// *Arguments*
/// mesh_function (_MeshFunction_)
/// A _MeshFunction_ object used to construct a
/// MeshValueCollection.
MeshValueCollection<T>& operator=(const MeshFunction<T>& mesh_function);
/// Assignment operator
///
/// *Arguments*
/// mesh_value_collection (_MeshValueCollection_)
/// A _MeshValueCollection_ object used to construct a
/// MeshValueCollection.
MeshValueCollection<T>&
operator=(const MeshValueCollection<T>& mesh_value_collection);
/// Initialise MeshValueCollection wirth mesh and dimension
///
/// *Arguments*
/// mesh (_mesh))
/// The mesh on which the value collection is defined
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
void init(const Mesh& mesh, std::size_t dim);
/// Initialise MeshValueCollection wirth mesh and dimension
/// (shared_ptr version)
///
/// *Arguments*
/// mesh (_mesh))
/// The mesh on which the value collection is defined
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
void init(boost::shared_ptr<const Mesh> mesh, std::size_t dim);
/// Set dimension. This function should not generally be used. It is
/// for reading MeshValueCollections as the dimension is not
/// generally known at construction.
///
/// *Arguments*
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
void init(std::size_t dim);
/// Return topological dimension
///
/// *Returns*
/// std::size_t
/// The dimension.
std::size_t dim() const;
/// Return associated mesh
///
/// *Returns*
/// _Mesh_
/// The mesh.
boost::shared_ptr<const Mesh> mesh() const;
/// Return true if the subset is empty
///
/// *Returns*
/// bool
/// True if the subset is empty.
bool empty() const;
/// Return size (number of entities in subset)
///
/// *Returns*
/// std::size_t
/// The size.
std::size_t size() const;
/// Set marker value for given entity defined by a cell index and
/// a local entity index
///
/// *Arguments*
/// cell_index (std::size_t)
/// The index of the cell.
/// local_entity (std::size_t)
/// The local index of the entity relative to the cell.
/// marker_value (T)
/// The value of the marker.
///
/// *Returns*
/// bool
/// True is a new value is inserted, false if overwriting
/// an existing value.
bool set_value(std::size_t cell_index, std::size_t local_entity,
const T& value);
/// Set value for given entity index
///
/// *Arguments*
/// entity_index (std::size_t)
/// Index of the entity.
/// value (T).
/// The value of the marker.
/// mesh (_Mesh_)
/// The mesh.
///
/// *Returns*
/// bool
/// True is a new value is inserted, false if overwriting
/// an existing value.
bool set_value(std::size_t entity_index, const T& value);
/// Get marker value for given entity defined by a cell index and
/// a local entity index
///
/// *Arguments*
/// cell_index (std::size_t)
/// The index of the cell.
/// local_entity (std::size_t)
/// The local index of the entity relative to the cell.
///
/// *Returns*
/// marker_value (T)
/// The value of the marker.
T get_value(std::size_t cell_index, std::size_t local_entity);
/// Get all values
///
/// *Returns*
/// std::map<std::pair<std::size_t, std::size_t>, T>
/// A map from positions to values.
std::map<std::pair<std::size_t, std::size_t>, T>& values();
/// Get all values (const version)
///
/// *Returns*
/// std::map<std::pair<std::size_t, std::size_t>, T>
/// A map from positions to values.
const std::map<std::pair<std::size_t, std::size_t>, T>& values() const;
/// Clear all values
void clear();
/// Return informal string representation (pretty-print)
///
/// *Arguments*
/// verbose (bool)
/// Flag to turn on additional output.
///
/// *Returns*
/// std::string
/// An informal representation.
std::string str(bool verbose) const;
private:
// Associated mesh
boost::shared_ptr<const Mesh> _mesh;
// Topological dimension
int _dim;
// The values
std::map<std::pair<std::size_t, std::size_t>, T> _values;
};
//---------------------------------------------------------------------------
// Implementation of MeshValueCollection
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection()
: Variable("m", "unnamed MeshValueCollection"), _dim(-1)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(boost::shared_ptr<const Mesh>
mesh) : _mesh(mesh), _dim(-1)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(const Mesh& mesh,
std::size_t dim)
: Variable("m", "unnamed MeshValueCollection"),
_mesh(reference_to_no_delete_pointer(mesh)), _dim(dim)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(boost::shared_ptr<const Mesh>
mesh, std::size_t dim)
: Variable("m", "unnamed MeshValueCollection"), _mesh(mesh), _dim(dim)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(const MeshFunction<T>&
mesh_function)
: Variable("m", "unnamed MeshValueCollection"), _mesh(mesh_function.mesh()),
_dim(mesh_function.dim())
{
dolfin_assert(_mesh);
const std::size_t D = _mesh->topology().dim();
// Handle cells as a special case
if ((int) D == _dim)
{
for (std::size_t cell_index = 0; cell_index < mesh_function.size();
++cell_index)
{
const std::pair<std::size_t, std::size_t> key(cell_index, 0);
_values.insert(std::make_pair(key, mesh_function[cell_index]));
}
}
else
{
_mesh->init(_dim, D);
const MeshConnectivity& connectivity = _mesh->topology()(_dim, D);
dolfin_assert(!connectivity.empty());
for (std::size_t entity_index = 0; entity_index < mesh_function.size();
++entity_index)
{
// Find the cell
dolfin_assert(connectivity.size(entity_index) > 0);
const MeshEntity entity(*_mesh, _dim, entity_index);
for (std::size_t i = 0; i < entity.num_entities(D) ; ++i)
{
// Create cell
const Cell cell(*_mesh, connectivity(entity_index)[i]);
// Find the local entity index
const std::size_t local_entity = cell.index(entity);
// Insert into map
const std::pair<std::size_t, std::size_t> key(cell.index(),
local_entity);
_values.insert(std::make_pair(key, mesh_function[entity_index]));
}
}
}
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(const Mesh& mesh,
const std::string filename)
: Variable("m", "unnamed MeshValueCollection"),
_mesh(reference_to_no_delete_pointer(mesh)), _dim(-1)
{
File file(filename);
file >> *this;
dolfin_assert(_dim > -1);
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>&
MeshValueCollection<T>::operator=(const MeshFunction<T>& mesh_function)
{
_mesh = mesh_function.mesh();
_dim = mesh_function.dim();
dolfin_assert(_mesh);
const std::size_t D = _mesh->topology().dim();
// FIXME: Use iterators
// Handle cells as a special case
if ((int) D == _dim)
{
for (std::size_t cell_index = 0; cell_index < mesh_function.size();
++cell_index)
{
const std::pair<std::size_t, std::size_t> key(cell_index, 0);
_values.insert(std::make_pair(key, mesh_function[cell_index]));
}
}
else
{
_mesh->init(_dim, D);
const MeshConnectivity& connectivity = _mesh->topology()(_dim, D);
dolfin_assert(!connectivity.empty());
for (std::size_t entity_index = 0; entity_index < mesh_function.size();
++entity_index)
{
// Find the cell
dolfin_assert(connectivity.size(entity_index) > 0);
const MeshEntity entity(*_mesh, _dim, entity_index);
for (std::size_t i = 0; i < entity.num_entities(D) ; ++i)
{
// Create cell
const Cell cell(*_mesh, connectivity(entity_index)[i]);
// Find the local entity index
const std::size_t local_entity = cell.index(entity);
// Insert into map
const std::pair<std::size_t, std::size_t> key(cell.index(),
local_entity);
_values.insert(std::make_pair(key, mesh_function[entity_index]));
}
}
}
return *this;
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>&
MeshValueCollection<T>::operator=(const MeshValueCollection<T>&
mesh_value_collection)
{
_mesh = mesh_value_collection._mesh;
_dim = mesh_value_collection.dim();
_values = mesh_value_collection.values();
return *this;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshValueCollection<T>::init(const Mesh& mesh, std::size_t dim)
{
mesh.init(dim);
_mesh = reference_to_no_delete_pointer(mesh);
_dim = dim;
_values.clear();
}
//---------------------------------------------------------------------------
template <typename T>
void MeshValueCollection<T>::init(boost::shared_ptr<const Mesh> mesh,
std::size_t dim)
{
mesh->init(dim);
_mesh = mesh;
_dim = dim;
_values.clear();
}
//---------------------------------------------------------------------------
template <typename T>
void MeshValueCollection<T>::init(std::size_t dim)
{
dolfin_assert(_mesh);
dolfin_assert(_dim < 0);
_dim = dim;
}
//---------------------------------------------------------------------------
template <typename T>
std::size_t MeshValueCollection<T>::dim() const
{
dolfin_assert(_dim >= 0);
return _dim;
}
//---------------------------------------------------------------------------
template <typename T>
bool MeshValueCollection<T>::empty() const
{
return _values.empty();
}
//---------------------------------------------------------------------------
template <typename T>
std::size_t MeshValueCollection<T>::size() const
{
return _values.size();
}
//---------------------------------------------------------------------------
template <typename T>
boost::shared_ptr<const Mesh> MeshValueCollection<T>::mesh() const
{
dolfin_assert(_mesh);
return _mesh;
}
//---------------------------------------------------------------------------
template <typename T>
bool MeshValueCollection<T>::set_value(std::size_t cell_index,
std::size_t local_entity,
const T& value)
{
dolfin_assert(_dim >= 0);
if (!_mesh)
{
dolfin_error("MeshValueCollection.h",
"set value",
"A mesh has not been associcated with this MeshValueCollection");
}
const std::pair<std::size_t, std::size_t> pos(cell_index, local_entity);
std::pair<typename std::map<std::pair<std::size_t,
std::size_t>, T>::iterator, bool> it;
it = _values.insert(std::make_pair(pos, value));
// If an item with same key already exists the value has not been
// set and we need to update it
if (!it.second)
it.first->second = value;
return it.second;
}
//---------------------------------------------------------------------------
template <typename T>
bool MeshValueCollection<T>::set_value(std::size_t entity_index,
const T& value)
{
if (!_mesh)
{
dolfin_error("MeshValueCollection.h",
"set value",
"A mesh has not been associcated with this MeshValueCollection");
}
dolfin_assert(_dim >= 0);
// Special case when d = D
const std::size_t D = _mesh->topology().dim();
if (_dim == (int) D)
{
// Set local entity index to zero when we mark a cell
const std::pair<std::size_t, std::size_t> pos(entity_index, 0);
std::pair<typename std::map<std::pair<std::size_t,
std::size_t>, T>::iterator, bool> it;
it = _values.insert(std::make_pair(pos, value));
// If an item with same key already exists the value has not been
// set and we need to update it
if (!it.second)
it.first->second = value;
return it.second;
}
// Get mesh connectivity d --> D
_mesh->init(_dim, D);
const MeshConnectivity& connectivity = _mesh->topology()(_dim, D);
// Find the cell
dolfin_assert(!connectivity.empty());
dolfin_assert(connectivity.size(entity_index) > 0);
const MeshEntity entity(*_mesh, _dim, entity_index);
const Cell cell(*_mesh, connectivity(entity_index)[0]); // choose first
// Find the local entity index
const std::size_t local_entity = cell.index(entity);
// Add value
const std::pair<std::size_t, std::size_t> pos(cell.index(), local_entity);
std::pair<typename std::map<std::pair<std::size_t,
std::size_t>, T>::iterator, bool> it;
it = _values.insert(std::make_pair(pos, value));
// If an item with same key already exists the value has not been
// set and we need to update it
if (!it.second)
it.first->second = value;
return it.second;
}
//---------------------------------------------------------------------------
template <typename T>
T MeshValueCollection<T>::get_value(std::size_t cell_index,
std::size_t local_entity)
{
dolfin_assert(_dim >= 0);
const std::pair<std::size_t, std::size_t> pos(cell_index, local_entity);
const typename std::map<std::pair<std::size_t,
std::size_t>, T>::const_iterator
it = _values.find(pos);
if (it == _values.end())
{
dolfin_error("MeshValueCollection.h",
"extract value",
"No value stored for cell index: %d and local index: %d",
cell_index, local_entity);
}
return it->second;
}
//---------------------------------------------------------------------------
template <typename T>
std::map<std::pair<std::size_t, std::size_t>, T>&
MeshValueCollection<T>::values()
{
return _values;
}
//---------------------------------------------------------------------------
template <typename T>
const std::map<std::pair<std::size_t, std::size_t>, T>&
MeshValueCollection<T>::values() const
{
return _values;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshValueCollection<T>::clear()
{
_values.clear();
}
//---------------------------------------------------------------------------
template <typename T>
std::string MeshValueCollection<T>::str(bool verbose) const
{
std::stringstream s;
if (verbose)
{
s << str(false) << std::endl << std::endl;
warning("Verbose output of MeshValueCollection must be implemented manually.");
}
else
{
s << "<MeshValueCollection of topological dimension " << dim()
<< " containing " << size() << " values>";
}
return s.str();
}
//---------------------------------------------------------------------------
}
#endif
|