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field_fe.cc
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1 /*!
2  *
3  * Copyright (C) 2015 Technical University of Liberec. All rights reserved.
4  *
5  * This program is free software; you can redistribute it and/or modify it under
6  * the terms of the GNU General Public License version 3 as published by the
7  * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
8  *
9  * This program is distributed in the hope that it will be useful, but WITHOUT
10  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11  * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
12  *
13  *
14  * @file field_fe.cc
15  * @brief
16  */
17 
18 
19 #include <limits>
20 
21 #include "fields/field_fe.hh"
22 #include "la/vector_mpi.hh"
23 #include "fields/field_instances.hh" // for instantiation macros
25 #include "input/input_type.hh"
26 #include "fem/fe_p.hh"
27 #include "fem/fe_system.hh"
28 #include "fem/dh_cell_accessor.hh"
29 #include "fem/mapping_p1.hh"
30 #include "io/reader_cache.hh"
31 #include "io/msh_gmshreader.h"
32 #include "mesh/accessors.hh"
33 #include "mesh/range_wrapper.hh"
34 #include "mesh/bc_mesh.hh"
36 
37 #include "system/sys_profiler.hh"
38 #include "tools/unit_converter.hh"
42 
43 
44 
45 
46 /// Implementation.
47 
48 namespace it = Input::Type;
49 
50 
51 
52 
54 
55 
56 
57 /************************************************************************************
58  * Implementation of FieldFE methods
59  */
60 template <int spacedim, class Value>
62 {
63  return it::Record("FieldFE", FieldAlgorithmBase<spacedim,Value>::template_name()+" Field given by finite element approximation.")
67  "GMSH mesh with data. Can be different from actual computational mesh.")
69  "Section where to find the field.\n Some sections are specific to file format: "
70  "point_data/node_data, cell_data/element_data, -/element_node_data, native/-.\n"
71  "If not given by a user, we try to find the field in all sections, but we report an error "
72  "if it is found in more than one section.")
74  "The values of the Field are read from the ```$ElementData``` section with field name given by this key.")
75  .declare_key("default_value", IT::Double(), IT::Default::optional(),
76  "Default value is set on elements which values have not been listed in the mesh data file.")
78  "Definition of the unit of all times defined in the mesh data file.")
79  .declare_key("read_time_shift", TimeGovernor::get_input_time_type(), IT::Default("0.0"),
80  "This key allows reading field data from the mesh data file shifted in time. Considering the time 't', field descriptor with time 'T', "
81  "time shift 'S', then if 't > T', we read the time frame 't + S'.")
83  IT::Default("\"equivalent_mesh\""), "Type of interpolation applied to the input spatial data.\n"
84  "The default value 'equivalent_mesh' assumes the data being constant on elements living on the same mesh "
85  "as the computational mesh, but possibly with different numbering. In the case of the same numbering, "
86  "the user can set 'identical_mesh' to omit algorithm for guessing node and element renumbering. "
87  "Alternatively, in case of different input mesh, several interpolation algorithms are available.")
88  .close();
89 }
90 
91 template <int spacedim, class Value>
93 {
94  return it::Selection("FE_discretization",
95  "Specify the section in mesh input file where field data is listed.\nSome sections are specific to file format.")
96  .add_value(OutputTime::DiscreteSpace::NODE_DATA, "node_data", "point_data (VTK) / node_data (GMSH)")
97  .add_value(OutputTime::DiscreteSpace::ELEM_DATA, "element_data", "cell_data (VTK) / element_data (GMSH)")
98  .add_value(OutputTime::DiscreteSpace::CORNER_DATA, "element_node_data", "element_node_data (only for GMSH)")
99  .add_value(OutputTime::DiscreteSpace::NATIVE_DATA, "native_data", "native_data (only for VTK)")
100  .close();
101 }
102 
103 template <int spacedim, class Value>
105 {
106  return it::Selection("interpolation", "Specify interpolation of the input data from its input mesh to the computational mesh.")
107  .add_value(DataInterpolation::identic_msh, "identic_mesh", "Topology and indices of nodes and elements of"
108  "the input mesh and the computational mesh are identical. "
109  "This interpolation is typically used for GMSH input files containing only the field values without "
110  "explicit mesh specification.")
111  .add_value(DataInterpolation::equivalent_msh, "equivalent_mesh", "Topologies of the input mesh and the computational mesh "
112  "are the same, the node and element numbering may differ. "
113  "This interpolation can be used also for VTK input data.") // default value
114  .add_value(DataInterpolation::gauss_p0, "P0_gauss", "Topologies of the input mesh and the computational mesh may differ. "
115  "Constant values on the elements of the computational mesh are evaluated using the Gaussian quadrature of the fixed order 4, "
116  "where the quadrature points and their values are found in the input mesh and input data using the BIH tree search."
117  )
118  .add_value(DataInterpolation::interp_p0, "P0_intersection", "Topologies of the input mesh and the computational mesh may differ. "
119  "Can be applied only for boundary fields. For every (boundary) element of the computational mesh the "
120  "intersection with the input mesh is computed. Constant values on the elements of the computational mesh "
121  "are evaluated as the weighted average of the (constant) values on the intersecting elements of the input mesh.")
122  .close();
123 }
124 
125 template <int spacedim, class Value>
127  Input::register_class< FieldFE<spacedim, Value>, unsigned int >("FieldFE") +
129 
130 
131 
132 template <int spacedim, class Value>
134 : FieldAlgorithmBase<spacedim, Value>(n_comp),
135  dh_(nullptr), field_name_(""), discretization_(OutputTime::DiscreteSpace::UNDEFINED), fe_values_(4)
136 {
137  this->is_constant_in_space_ = false;
138 }
139 
140 
141 template<int spacedim, class Value>
143  Input::Array multifield_arr;
144  if (rec.opt_val(field.input_name(), multifield_arr))
145  {
146  unsigned int position = 0;
147  auto it = multifield_arr.begin<Input::AbstractRecord>();
148  if (multifield_arr.size() > 1)
149  while (index_ != position) {
150  ++it; ++position;
151  }
152 
153  Input::Record field_rec = (Input::Record)(*it);
154  if (field_rec.val<std::string>("TYPE") == "FieldFE") {
155  OutputTime::DiscreteSpace discretization;
156  if (field_rec.opt_val<OutputTime::DiscreteSpace>("input_discretization", discretization)) {
157  if (discretization == OutputTime::DiscreteSpace::NATIVE_DATA) {
158  std::shared_ptr< FieldFE<spacedim, Value> > field_fe = std::make_shared< FieldFE<spacedim, Value> >(field.n_comp());
159  FieldAlgoBaseInitData init_data(field.input_name(), field.n_comp(), field.units(), field.limits(), field.get_flags());
160  field_fe->init_from_input( *it, init_data );
161  field_fe->set_fe_data(conc_dof_handler_, dof_vector_);
162  return field_fe;
163  }
164  }
165  }
166  }
167 
168  return NULL;
169 }
170 
171 
172 template <int spacedim, class Value>
173 VectorMPI FieldFE<spacedim, Value>::set_fe_data(std::shared_ptr<DOFHandlerMultiDim> dh, VectorMPI dof_values, unsigned int block_index)
174 {
175  dh_ = dh;
176  if (dof_values.size()==0) { //create data vector according to dof handler - Warning not tested yet
177  data_vec_ = dh_->create_vector();
179  } else {
180  data_vec_ = dof_values;
181  }
182 
183  if ( block_index == FieldFE<spacedim, Value>::undef_uint ) {
184  this->fill_fe_item<0>();
185  this->fill_fe_item<1>();
186  this->fill_fe_item<2>();
187  this->fill_fe_item<3>();
188  this->fe_ = dh_->ds()->fe();
189  } else {
190  this->fill_fe_system_data<0>(block_index);
191  this->fill_fe_system_data<1>(block_index);
192  this->fill_fe_system_data<2>(block_index);
193  this->fill_fe_system_data<3>(block_index);
195  std::dynamic_pointer_cast<FESystem<0>>( dh_->ds()->fe()[Dim<0>{}] )->fe()[block_index],
196  std::dynamic_pointer_cast<FESystem<1>>( dh_->ds()->fe()[Dim<1>{}] )->fe()[block_index],
197  std::dynamic_pointer_cast<FESystem<2>>( dh_->ds()->fe()[Dim<2>{}] )->fe()[block_index],
198  std::dynamic_pointer_cast<FESystem<3>>( dh_->ds()->fe()[Dim<3>{}] )->fe()[block_index]
199  );
200  }
201 
202  unsigned int ndofs = dh_->max_elem_dofs();
203 
204  // initialization data of value handlers
205  FEValueInitData init_data;
206  init_data.dh = dh_;
207  init_data.data_vec = data_vec_;
208  init_data.ndofs = ndofs;
209  init_data.n_comp = this->n_comp();
210  init_data.mixed_fe = this->fe_;
211 
212  // initialize value handler objects
213  init_data.range_begin = this->fe_item_[0].range_begin_;
214  init_data.range_end = this->fe_item_[0].range_end_;
215  value_handler0_.initialize(init_data);
216  init_data.range_begin = this->fe_item_[1].range_begin_;
217  init_data.range_end = this->fe_item_[1].range_end_;
218  value_handler1_.initialize(init_data);
219  init_data.range_begin = this->fe_item_[2].range_begin_;
220  init_data.range_end = this->fe_item_[2].range_end_;
221  value_handler2_.initialize(init_data);
222  init_data.range_begin = this->fe_item_[3].range_begin_;
223  init_data.range_end = this->fe_item_[3].range_end_;
224  value_handler3_.initialize(init_data);
225 
226  // set interpolation
227  interpolation_ = DataInterpolation::equivalent_msh;
228 
229  return data_vec_;
230 }
231 
232 
233 /**
234  * Returns one value in one given point. ResultType can be used to avoid some costly calculation if the result is trivial.
235  */
236 template <int spacedim, class Value>
237 typename Value::return_type const & FieldFE<spacedim, Value>::value(const Point &p, const ElementAccessor<spacedim> &elm)
238 {
239  switch (elm.dim()) {
240  case 0:
241  return value_handler0_.value(p, elm);
242  case 1:
243  return value_handler1_.value(p, elm);
244  case 2:
245  return value_handler2_.value(p, elm);
246  case 3:
247  return value_handler3_.value(p, elm);
248  default:
249  ASSERT_PERMANENT(false).error("Invalid element dimension!");
250  }
251 
252  return this->r_value_;
253 }
254 
255 
256 
257 /**
258  * Returns std::vector of scalar values in several points at once.
259  */
260 template <int spacedim, class Value>
263 {
264  ASSERT_EQ( point_list.size(), value_list.size() ).error();
265  ASSERT( point_list.n_rows() == spacedim && point_list.n_cols() == 1).error("Invalid point size.\n");
266 
267  switch (elm.dim()) {
268  case 0:
269  value_handler0_.value_list(point_list, elm, value_list);
270  break;
271  case 1:
272  value_handler1_.value_list(point_list, elm, value_list);
273  break;
274  case 2:
275  value_handler2_.value_list(point_list, elm, value_list);
276  break;
277  case 3:
278  value_handler3_.value_list(point_list, elm, value_list);
279  break;
280  default:
281  ASSERT_PERMANENT(false).error("Invalid element dimension!");
282  }
283 }
284 
285 
286 
287 template <int spacedim, class Value>
289  ElementCacheMap &cache_map, unsigned int region_patch_idx)
290 {
291  ASSERT( !boundary_dofs_ ).error("boundary field NOT supported!!\n");
293 
294  unsigned int reg_chunk_begin = cache_map.region_chunk_begin(region_patch_idx);
295  unsigned int reg_chunk_end = cache_map.region_chunk_end(region_patch_idx);
296  unsigned int last_element_idx = -1;
297  DHCellAccessor cell = *( dh_->local_range().begin() ); //needs set variable for correct compiling
298  LocDofVec loc_dofs;
299  unsigned int range_bgn=0, range_end=0;
300 
301  for (unsigned int i_data = reg_chunk_begin; i_data < reg_chunk_end; ++i_data) { // i_eval_point_data
302  unsigned int elm_idx = cache_map.eval_point_data(i_data).i_element_;
303  if (elm_idx != last_element_idx) {
304  ElementAccessor<spacedim> elm(dh_->mesh(), elm_idx);
305  fe_values_[elm.dim()].reinit( elm );
306  cell = dh_->cell_accessor_from_element( elm_idx );
307  loc_dofs = cell.get_loc_dof_indices();
308  last_element_idx = elm_idx;
309  range_bgn = this->fe_item_[elm.dim()].range_begin_;
310  range_end = this->fe_item_[elm.dim()].range_end_;
311  }
312 
313  unsigned int i_ep=cache_map.eval_point_data(i_data).i_eval_point_;
314  //DHCellAccessor cache_cell = cache_map(cell);
315  mat_value.fill(0.0);
316  for (unsigned int i_dof=range_bgn, i_cdof=0; i_dof<range_end; i_dof++, i_cdof++) {
317  mat_value += data_vec_.get(loc_dofs[i_dof]) * this->handle_fe_shape(cell.dim(), i_cdof, i_ep);
318  }
319  data_cache.set(i_data) = mat_value;
320  }
321 }
322 
323 
324 template <int spacedim, class Value>
326 {
327  std::shared_ptr<EvalPoints> eval_points = cache_map.eval_points();
328  std::array<Quadrature, 4> quads{QGauss(0, 1), this->init_quad<1>(eval_points), this->init_quad<2>(eval_points), this->init_quad<3>(eval_points)};
329  fe_values_[0].initialize(quads[0], *this->fe_[0_d], update_values);
330  fe_values_[1].initialize(quads[1], *this->fe_[1_d], update_values);
331  fe_values_[2].initialize(quads[2], *this->fe_[2_d], update_values);
332  fe_values_[3].initialize(quads[3], *this->fe_[3_d], update_values);
333 }
334 
335 
336 template <int spacedim, class Value>
337 template <unsigned int dim>
338 Quadrature FieldFE<spacedim, Value>::init_quad(std::shared_ptr<EvalPoints> eval_points)
339 {
340  Quadrature quad(dim, eval_points->size(dim));
341  for (unsigned int k=0; k<eval_points->size(dim); k++)
342  quad.set(k) = eval_points->local_point<dim>(k);
343  return quad;
344 }
345 
346 
347 template <int spacedim, class Value>
349  this->init_unit_conversion_coefficient(rec, init_data);
350  this->in_rec_ = rec;
351  flags_ = init_data.flags_;
352 
353 
354  // read data from input record
355  reader_file_ = FilePath( rec.val<FilePath>("mesh_data_file") );
356  field_name_ = rec.val<std::string>("field_name");
357  if (! rec.opt_val<OutputTime::DiscreteSpace>("input_discretization", discretization_) ) {
358  discretization_ = OutputTime::DiscreteSpace::UNDEFINED;
359  }
360  if (! rec.opt_val<DataInterpolation>("interpolation", interpolation_) ) {
361  interpolation_ = DataInterpolation::equivalent_msh;
362  }
363  if (! rec.opt_val("default_value", default_value_) ) {
364  default_value_ = numeric_limits<double>::signaling_NaN();
365  }
366 }
367 
368 
369 
370 template <int spacedim, class Value>
371 void FieldFE<spacedim, Value>::set_mesh(const Mesh *mesh, bool boundary_domain) {
372  // Mesh can be set only for field initialized from input.
374  ASSERT(field_name_ != "").error("Uninitialized FieldFE, did you call init_from_input()?\n");
375  this->boundary_domain_ = boundary_domain;
376  if (this->interpolation_ == DataInterpolation::identic_msh) {
378  } else {
379  auto source_mesh = ReaderCache::get_mesh(reader_file_);
380  ReaderCache::get_element_ids(reader_file_, *(source_mesh.get()));
381  if (this->interpolation_ == DataInterpolation::equivalent_msh) {
383  if (source_target_mesh_elm_map_->empty()) { // incompatible meshes
384  this->interpolation_ = DataInterpolation::gauss_p0;
385  WarningOut().fmt("Source mesh of FieldFE '{}' is not compatible with target mesh.\nInterpolation of input data will be changed to 'P0_gauss'.\n",
386  field_name_);
387  }
388  } else if (this->interpolation_ == DataInterpolation::interp_p0) {
389  if (!boundary_domain) {
390  this->interpolation_ = DataInterpolation::gauss_p0;
391  WarningOut().fmt("Interpolation 'P0_intersection' of FieldFE '{}' can't be used on bulk region.\nIt will be changed to 'P0_gauss'.\n",
392  field_name_);
393  }
394  }
395  }
396  if (dh_ == nullptr) {
397  if (boundary_domain) this->make_dof_handler( mesh->bc_mesh() );
398  else this->make_dof_handler( mesh );
399  }
400  }
401 }
402 
403 
404 
405 template <int spacedim, class Value>
407  ASSERT(this->boundary_domain_);
408 
409  auto bc_mesh = dh_->mesh()->bc_mesh();
410  unsigned int n_comp = this->value_.n_rows() * this->value_.n_cols();
411  boundary_dofs_ = std::make_shared< std::vector<IntIdx> >( n_comp * bc_mesh->n_elements() );
412  std::vector<IntIdx> &in_vec = *( boundary_dofs_.get() );
413  unsigned int j = 0; // actual index to boundary_dofs_ vector
414 
415  for (auto ele : bc_mesh->elements_range()) {
416  IntIdx elm_shift = n_comp * ele.idx();
417  for (unsigned int i=0; i<n_comp; ++i, ++j) {
418  in_vec[j] = elm_shift + i;
419  }
420  }
421 
426 
428 }
429 
430 
431 
432 template <int spacedim, class Value>
434 
435  // temporary solution - these objects will be set through FieldCommon
437  switch (this->value_.n_rows() * this->value_.n_cols()) { // by number of components
438  case 1: { // scalar
439  fe = MixedPtr<FE_P_disc>(0);
440  break;
441  }
442  case 3: { // vector
443  MixedPtr<FE_P_disc> fe_base(0) ;
444  fe = mixed_fe_system(fe_base, FEType::FEVector, 3);
445  break;
446  }
447  case 9: { // tensor
448  MixedPtr<FE_P_disc> fe_base(0) ;
449  fe = mixed_fe_system(fe_base, FEType::FETensor, 9);
450  break;
451  }
452  default:
453  ASSERT_PERMANENT(false).error("Should not happen!\n");
454  }
455 
456  std::shared_ptr<DOFHandlerMultiDim> dh_par = std::make_shared<DOFHandlerMultiDim>( const_cast<MeshBase &>(*mesh) );
457  std::shared_ptr<DiscreteSpace> ds = std::make_shared<EqualOrderDiscreteSpace>( &const_cast<MeshBase &>(*mesh), fe);
458  dh_par->distribute_dofs(ds);
459  dh_ = dh_par;
460  unsigned int ndofs = dh_->max_elem_dofs();
461 
462  this->fill_fe_item<0>();
463  this->fill_fe_item<1>();
464  this->fill_fe_item<2>();
465  this->fill_fe_item<3>();
466  this->fe_ = dh_->ds()->fe();
467 
468  data_vec_ = VectorMPI::sequential( dh_->lsize() ); // allocate data_vec_
469 
470  // initialization data of value handlers
471  FEValueInitData init_data;
472  init_data.dh = dh_;
473  init_data.data_vec = data_vec_;
474  init_data.ndofs = ndofs;
475  init_data.n_comp = this->n_comp();
476  init_data.mixed_fe = this->fe_;
477 
478  // initialize value handler objects
479  init_data.range_begin = this->fe_item_[0].range_begin_;
480  init_data.range_end = this->fe_item_[0].range_end_;
481  value_handler0_.initialize(init_data);
482  init_data.range_begin = this->fe_item_[1].range_begin_;
483  init_data.range_end = this->fe_item_[1].range_end_;
484  value_handler1_.initialize(init_data);
485  init_data.range_begin = this->fe_item_[2].range_begin_;
486  init_data.range_end = this->fe_item_[2].range_end_;
487  value_handler2_.initialize(init_data);
488  init_data.range_begin = this->fe_item_[3].range_begin_;
489  init_data.range_end = this->fe_item_[3].range_end_;
490  value_handler3_.initialize(init_data);
491 }
492 
493 
494 
495 template <int spacedim, class Value>
497  // Time can be set only for field initialized from input.
499  ASSERT(field_name_ != "").error("Uninitialized FieldFE, did you call init_from_input()?\n");
500  ASSERT_PTR(dh_)(field_name_).error("Null target mesh pointer of finite element field, did you call set_mesh()?\n");
501  if ( reader_file_ == FilePath() ) return false;
502 
503  unsigned int n_components = this->value_.n_rows() * this->value_.n_cols();
504  double time_unit_coef = time.read_coef(in_rec_.find<Input::Record>("time_unit"));
505  double time_shift = time.read_time( in_rec_.find<Input::Tuple>("read_time_shift") );
506  double read_time = (time.end()+time_shift) / time_unit_coef;
507 
508  unsigned int n_entities;
509  bool is_native = (this->discretization_ == OutputTime::DiscreteSpace::NATIVE_DATA);
510  bool boundary;
511  if (is_native || this->interpolation_==DataInterpolation::identic_msh || this->interpolation_==DataInterpolation::equivalent_msh) {
512  boundary = this->boundary_domain_;
513  } else {
514  boundary = false;
515  }
516  if (is_native) {
517  n_entities = dh_->mesh()->n_elements();
518  n_components *= dh_->max_elem_dofs();
519  } else if (this->interpolation_==DataInterpolation::identic_msh) {
520  n_entities = dh_->mesh()->n_elements();
521  } else {
522  auto reader_mesh = ReaderCache::get_mesh(reader_file_);
523  n_entities = boundary ? reader_mesh->bc_mesh()->n_elements() : reader_mesh->n_elements();
524  }
525 
526  BaseMeshReader::HeaderQuery header_query(field_name_, read_time, this->discretization_, dh_->hash());
527  auto reader = ReaderCache::get_reader(reader_file_);
528  auto header = reader->find_header(header_query);
529  auto input_data_cache = reader->template get_element_data<double>(
530  header, n_entities, n_components, boundary);
531  CheckResult checked_data = reader->scale_and_check_limits(field_name_,
532  this->unit_conversion_coefficient_, default_value_);
533 
534 
535  if ( !is_native && (checked_data == CheckResult::not_a_number) ) {
536  THROW( ExcUndefElementValue() << EI_Field(field_name_) );
537  }
538 
539  if (is_native) {
540  this->calculate_native_values(input_data_cache);
541  } else if (this->interpolation_==DataInterpolation::identic_msh) {
542  this->calculate_identic_values(input_data_cache);
543  } else if (this->interpolation_==DataInterpolation::equivalent_msh) {
544  this->calculate_equivalent_values(input_data_cache);
545  } else if (this->interpolation_==DataInterpolation::gauss_p0) {
546  this->interpolate_gauss(input_data_cache);
547  } else { // DataInterpolation::interp_p0
548  this->interpolate_intersection(input_data_cache);
549  }
550 
551  return true;
552  } else return false;
553 
554 }
555 
556 
557 template <int spacedim, class Value>
559 {
560  static const unsigned int quadrature_order = 4; // parameter of quadrature
561  std::shared_ptr<Mesh> source_mesh = ReaderCache::get_mesh(reader_file_);
562  std::vector<unsigned int> searched_elements; // stored suspect elements in calculating the intersection
563  std::vector<arma::vec::fixed<3>> q_points; // real coordinates of quadrature points
564  std::vector<double> q_weights; // weights of quadrature points
565  unsigned int quadrature_size=0; // size of quadrature point and weight vector
566  std::vector<double> sum_val(dh_->max_elem_dofs()); // sum of value of one quadrature point
567  unsigned int elem_count; // count of intersect (source) elements of one quadrature point
568  std::vector<double> elem_value(dh_->max_elem_dofs()); // computed value of one (target) element
569  bool contains; // sign if source element contains quadrature point
570 
571  {
572  // set size of vectors to maximal count of quadrature points
573  QGauss quad(3, quadrature_order);
574  q_points.resize(quad.size());
575  q_weights.resize(quad.size());
576  }
577 
578  for (auto cell : dh_->own_range()) {
579  auto ele = cell.elm();
580  std::fill(elem_value.begin(), elem_value.end(), 0.0);
581  switch (cell.dim()) {
582  case 0:
583  quadrature_size = 1;
584  q_points[0] = *ele.node(0);
585  q_weights[0] = 1.0;
586  break;
587  case 1:
588  quadrature_size = value_handler1_.compute_quadrature(q_points, q_weights, ele, quadrature_order);
589  break;
590  case 2:
591  quadrature_size = value_handler2_.compute_quadrature(q_points, q_weights, ele, quadrature_order);
592  break;
593  case 3:
594  quadrature_size = value_handler3_.compute_quadrature(q_points, q_weights, ele, quadrature_order);
595  break;
596  }
597  searched_elements.clear();
598  source_mesh->get_bih_tree().find_bounding_box(ele.bounding_box(), searched_elements);
599 
600  for (unsigned int i=0; i<quadrature_size; ++i) {
601  std::fill(sum_val.begin(), sum_val.end(), 0.0);
602  elem_count = 0;
603  for (std::vector<unsigned int>::iterator it = searched_elements.begin(); it!=searched_elements.end(); it++) {
604  ElementAccessor<3> elm = source_mesh->element_accessor(*it);
605  contains=false;
606  switch (elm->dim()) {
607  case 0:
608  contains = arma::norm(*elm.node(0) - q_points[i], 2) < 4*std::numeric_limits<double>::epsilon();
609  break;
610  case 1:
611  contains = MappingP1<1,3>::contains_point(q_points[i], elm);
612  break;
613  case 2:
614  contains = MappingP1<2,3>::contains_point(q_points[i], elm);
615  break;
616  case 3:
617  contains = MappingP1<3,3>::contains_point(q_points[i], elm);
618  break;
619  default:
620  ASSERT_PERMANENT(false).error("Invalid element dimension!");
621  }
622  if ( contains ) {
623  // projection point in element
624  unsigned int index = sum_val.size() * (*it);
625  for (unsigned int j=0; j < sum_val.size(); j++) {
626  sum_val[j] += (*data_vec)[index+j];
627  }
628  ++elem_count;
629  }
630  }
631 
632  if (elem_count > 0) {
633  for (unsigned int j=0; j < sum_val.size(); j++) {
634  elem_value[j] += (sum_val[j] / elem_count) * q_weights[i];
635  }
636  }
637  }
638 
639  LocDofVec loc_dofs;
640  loc_dofs = cell.get_loc_dof_indices();
641 
642  ASSERT_LE(loc_dofs.n_elem, elem_value.size());
643  for (unsigned int i=0; i < elem_value.size(); i++) {
644  ASSERT_LT( loc_dofs[i], (int)data_vec_.size());
645  data_vec_.set( loc_dofs[i], elem_value[i] * this->unit_conversion_coefficient_ );
646  }
647  }
648 }
649 
650 
651 template <int spacedim, class Value>
653 {
654  std::shared_ptr<Mesh> source_mesh = ReaderCache::get_mesh(reader_file_);
655  std::vector<unsigned int> searched_elements; // stored suspect elements in calculating the intersection
656  std::vector<double> value(dh_->max_elem_dofs());
657  double total_measure;
658  double measure = 0;
659 
660  for (auto elm : dh_->mesh()->elements_range()) {
661  if (elm.dim() == 3) {
662  THROW( ExcInvalidElemeDim() << EI_ElemIdx(elm.idx()) );
663  }
664 
665  double epsilon = 4* numeric_limits<double>::epsilon() * elm.measure();
666 
667  // gets suspect elements
668  if (elm.dim() == 0) {
669  searched_elements.clear();
670  source_mesh->get_bih_tree().find_point(*elm.node(0), searched_elements);
671  } else {
672  BoundingBox bb = elm.bounding_box();
673  searched_elements.clear();
674  source_mesh->get_bih_tree().find_bounding_box(bb, searched_elements);
675  }
676 
677  // set zero values of value object
678  std::fill(value.begin(), value.end(), 0.0);
679  total_measure=0.0;
680 
681  START_TIMER("compute_pressure");
682  ADD_CALLS(searched_elements.size());
683 
684 
685  for (std::vector<unsigned int>::iterator it = searched_elements.begin(); it!=searched_elements.end(); it++)
686  {
687  ElementAccessor<3> source_elm = source_mesh->element_accessor(*it);
688  if (source_elm->dim() == 3) {
689  // get intersection (set measure = 0 if intersection doesn't exist)
690  switch (elm.dim()) {
691  case 0: {
692  arma::vec::fixed<3> real_point = *elm.node(0);
693  arma::mat::fixed<3, 4> elm_map = MappingP1<3,3>::element_map(source_elm);
694  arma::vec::fixed<4> unit_point = MappingP1<3,3>::project_real_to_unit(real_point, elm_map);
695 
696  measure = (std::fabs(arma::sum( unit_point )-1) <= 1e-14
697  && arma::min( unit_point ) >= 0)
698  ? 1.0 : 0.0;
699  break;
700  }
701  case 1: {
702  IntersectionAux<1,3> is(elm.idx(), source_elm.idx());
703  ComputeIntersection<1,3> CI(elm, source_elm);
704  CI.init();
705  CI.compute(is);
706 
707  IntersectionLocal<1,3> ilc(is);
708  measure = ilc.compute_measure() * elm.measure();
709  break;
710  }
711  case 2: {
712  IntersectionAux<2,3> is(elm.idx(), source_elm.idx());
713  ComputeIntersection<2,3> CI(elm, source_elm);
714  CI.init();
715  CI.compute(is);
716 
717  IntersectionLocal<2,3> ilc(is);
718  measure = 2 * ilc.compute_measure() * elm.measure();
719  break;
720  }
721  }
722 
723  //adds values to value_ object if intersection exists
724  if (measure > epsilon) {
725  unsigned int index = value.size() * (*it);
726  std::vector<double> &vec = *( data_vec.get() );
727  for (unsigned int i=0; i < value.size(); i++) {
728  value[i] += vec[index+i] * measure;
729  }
730  total_measure += measure;
731  }
732  }
733  }
734 
735  // computes weighted average, store it to data vector
736  if (total_measure > epsilon) {
737  DHCellAccessor cell = dh_->cell_accessor_from_element(elm.idx());
738  LocDofVec loc_dofs = cell.get_loc_dof_indices();
739 
740  ASSERT_LE(loc_dofs.n_elem, value.size());
741  for (unsigned int i=0; i < value.size(); i++) {
742  data_vec_.set(loc_dofs[i], value[i] / total_measure);
743  }
744  } else {
745  WarningOut().fmt("Processed element with idx {} is out of source mesh!\n", elm.idx());
746  }
747  END_TIMER("compute_pressure");
748 
749  }
750 }
751 
752 
753 template <int spacedim, class Value>
755 {
756  // Same algorithm as in output of Node_data. Possibly code reuse.
757  unsigned int dof_size, data_vec_i;
758  std::vector<unsigned int> count_vector(data_vec_.size(), 0);
760  std::vector<LongIdx> global_dof_indices(dh_->max_elem_dofs());
761  std::vector<LongIdx> &source_target_vec = (dynamic_cast<BCMesh*>(dh_->mesh()) != nullptr) ? source_target_mesh_elm_map_->boundary : source_target_mesh_elm_map_->bulk;
762 
763  // iterate through cells, assembly MPIVector
764  for (auto cell : dh_->own_range()) {
765  dof_size = cell.get_dof_indices(global_dof_indices);
766  LocDofVec loc_dofs = cell.get_loc_dof_indices();
767  data_vec_i = source_target_vec[cell.elm_idx()] * dof_size;
768  ASSERT_EQ(dof_size, loc_dofs.n_elem);
769  for (unsigned int i=0; i<dof_size; ++i, ++data_vec_i) {
770  data_vec_.add( loc_dofs[i], (*data_cache)[ data_vec_i ] );
771  ++count_vector[ loc_dofs[i] ];
772  }
773  }
774 
775  // compute averages of values
776  for (unsigned int i=0; i<data_vec_.size(); ++i) {
777  if (count_vector[i]>0) data_vec_.normalize(i, count_vector[i]);
778  }
779 }
780 
781 
782 template <int spacedim, class Value>
784 {
785  // Same algorithm as in output of Node_data. Possibly code reuse.
786  unsigned int data_vec_i;
787  std::vector<unsigned int> count_vector(data_vec_.size(), 0);
789 
790  // iterate through cells, assembly global vector and count number of writes - prepared solution for further development
791  for (auto cell : dh_->own_range()) {
792  LocDofVec loc_dofs = cell.get_loc_dof_indices();
793  data_vec_i = cell.elm_idx() * dh_->max_elem_dofs();
794  for (unsigned int i=0; i<loc_dofs.n_elem; ++i, ++data_vec_i) {
795  ASSERT_LT(loc_dofs[i], (LongIdx)data_vec_.size());
796  data_vec_.add( loc_dofs[i], (*data_cache)[data_vec_i] );
797  ++count_vector[ loc_dofs[i] ];
798  }
799  }
800 
801  // compute averages of values
802  for (unsigned int i=0; i<data_vec_.size(); ++i) {
803  if (count_vector[i]>0) data_vec_.normalize(i, count_vector[i]);
804  }
805 }
806 
807 
808 template <int spacedim, class Value>
810 {
811  // Same algorithm as in output of Node_data. Possibly code reuse.
812  unsigned int data_vec_i;
813  std::vector<unsigned int> count_vector(data_vec_.size(), 0);
815  std::vector<LongIdx> &source_target_vec = (dynamic_cast<BCMesh*>(dh_->mesh()) != nullptr) ? source_target_mesh_elm_map_->boundary : source_target_mesh_elm_map_->bulk;
816 
817  // iterate through elements, assembly global vector and count number of writes
818  for (auto cell : dh_->own_range()) {
819  LocDofVec loc_dofs = cell.get_loc_dof_indices();
820  if (source_target_vec[cell.elm_idx()] == (int)(Mesh::undef_idx)) { // undefined value in input data mesh
821  if ( std::isnan(default_value_) )
822  THROW( ExcUndefElementValue() << EI_Field(field_name_) );
823  for (unsigned int i=0; i<loc_dofs.n_elem; ++i) {
824  ASSERT_LT(loc_dofs[i], (LongIdx)data_vec_.size());
825  data_vec_.add( loc_dofs[i], default_value_ * this->unit_conversion_coefficient_ );
826  ++count_vector[ loc_dofs[i] ];
827  }
828  } else {
829  data_vec_i = source_target_vec[cell.elm_idx()] * dh_->max_elem_dofs();
830  for (unsigned int i=0; i<loc_dofs.n_elem; ++i, ++data_vec_i) {
831  ASSERT_LT(loc_dofs[i], (LongIdx)data_vec_.size());
832  data_vec_.add( loc_dofs[i], (*data_cache)[data_vec_i] );
833  ++count_vector[ loc_dofs[i] ];
834  }
835  }
836  }
837 
838  // compute averages of values
839  for (unsigned int i=0; i<data_vec_.size(); ++i) {
840  if (count_vector[i]>0) data_vec_.normalize(i, count_vector[i]);
841  }
842 }
843 
844 
845 template <int spacedim, class Value>
847  //ASSERT_EQ(output_data_cache.n_values() * output_data_cache.n_comp(), dh_->distr()->lsize()).error();
848  unsigned int n_vals = output_data_cache.n_comp() * output_data_cache.n_dofs_per_element();
849  double loc_values[n_vals];
850  unsigned int i;
851 
852  for (auto dh_cell : dh_->own_range()) {
853  LocDofVec loc_dofs = dh_cell.get_loc_dof_indices();
854  for (i=0; i<loc_dofs.n_elem; ++i) loc_values[i] = data_vec_.get( loc_dofs[i] );
855  for ( ; i<n_vals; ++i) loc_values[i] = numeric_limits<double>::signaling_NaN();
856  output_data_cache.store_value( dh_cell.local_idx(), loc_values );
857  }
858 
859  output_data_cache.set_dof_handler_hash( dh_->hash() );
860 }
861 
862 
863 
864 template <int spacedim, class Value>
865 inline unsigned int FieldFE<spacedim, Value>::data_size() const {
866  return data_vec_.size();
867 }
868 
869 
870 
871 template <int spacedim, class Value>
874 }
875 
876 
877 
878 template <int spacedim, class Value>
881 }
882 
883 
884 
885 /*template <int spacedim, class Value>
886 Armor::ArmaMat<typename Value::element_type, Value::NRows_, Value::NCols_> FieldFE<spacedim, Value>::handle_fe_shape(unsigned int dim,
887  unsigned int i_dof, unsigned int i_qp, unsigned int comp_index)
888 {
889  Armor::ArmaMat<typename Value::element_type, Value::NCols_, Value::NRows_> v;
890  for (unsigned int c=0; c<Value::NRows_*Value::NCols_; ++c)
891  v(c/spacedim,c%spacedim) = fe_values_[dim].shape_value_component(i_dof, i_qp, comp_index+c);
892  if (Value::NRows_ == Value::NCols_)
893  return v;
894  else
895  return v.t();
896 }*/
897 
898 
899 
900 template <int spacedim, class Value>
902 {}
903 
904 
905 // Instantiations of FieldFE
FieldCommon::units
FieldCommon & units(const UnitSI &units)
Set basic units of the field.
Definition: field_common.hh:152
EvalPointData::i_element_
unsigned int i_element_
mesh_idx of ElementAccessor appropriate to element
Definition: field_value_cache.hh:74
FieldFE::data_size
unsigned int data_size() const
Definition: field_fe.cc:865
TimeStep::read_coef
double read_coef(Input::Iterator< Input::Record > unit_it) const
Definition: time_governor.cc:268
ElementAccessor::dim
unsigned int dim() const
Definition: accessors.hh:188
LocDofVec
arma::Col< IntIdx > LocDofVec
Definition: index_types.hh:28
FieldFE::field_name_
std::string field_name_
field name read from input
Definition: field_fe.hh:282
FlagArray::match
constexpr bool match(Mask mask) const
Definition: flag_array.hh:163
FEValueInitData::range_end
unsigned int range_end
Holds end of component range of evaluation.
Definition: fe_value_handler.hh:48
FieldFE::boundary_dofs_
std::shared_ptr< std::vector< IntIdx > > boundary_dofs_
Definition: field_fe.hh:307
FieldFE::source_target_mesh_elm_map_
std::shared_ptr< EquivalentMeshMap > source_target_mesh_elm_map_
Maps element indices between source (data) and target (computational) mesh if data interpolation is s...
Definition: field_fe.hh:313
FieldFE::flags_
FieldFlag::Flags flags_
Field flags.
Definition: field_fe.hh:291
EvalPointData::i_eval_point_
unsigned int i_eval_point_
index of point in EvalPoint object
Definition: field_value_cache.hh:75
FieldFE::FieldFE
FieldFE(unsigned int n_comp=0)
Definition: field_fe.cc:133
FieldFE::NativeFactory::conc_dof_handler_
std::shared_ptr< DOFHandlerMultiDim > conc_dof_handler_
Definition: field_fe.hh:109
TimeUnitConversion::get_input_default
static Input::Type::Default get_input_default()
Definition: time_governor.hh:66
vector_mpi.hh
ComputeIntersection< 2, 3 >
Class for 2D-2D intersections.
Definition: compute_intersection.hh:465
FieldFE::local_to_ghost_data_scatter_end
void local_to_ghost_data_scatter_end()
Call end scatter functions (local to ghost) on data vector.
Definition: field_fe.cc:879
FieldFE::value_handler0_
FEValueHandler< 0, spacedim, Value > value_handler0_
Value handler that allows get value of 0D elements.
Definition: field_fe.hh:270
FieldFE::cache_update
void cache_update(FieldValueCache< typename Value::element_type > &data_cache, ElementCacheMap &cache_map, unsigned int region_patch_idx) override
Definition: field_fe.cc:288
FEValueHandler::initialize
void initialize(FEValueInitData init_data)
Initialize data members.
Definition: fe_value_handler.cc:93
FieldFE::handle_fe_shape
Armor::ArmaMat< typename Value::element_type, Value::NRows_, Value::NCols_ > handle_fe_shape(unsigned int dim, unsigned int i_dof, unsigned int i_qp)
Definition: field_fe.hh:234
ElementDataCache
Definition: element_data_cache.hh:44
ASSERT
#define ASSERT(expr)
Definition: asserts.hh:350
FieldFE::DataInterpolation
DataInterpolation
Definition: field_fe.hh:60
Element::dim
unsigned int dim() const
Definition: elements.h:120
bc_mesh.hh
FieldFE::calculate_native_values
void calculate_native_values(ElementDataCache< double >::CacheData data_cache)
Calculate native data over all elements of target mesh.
Definition: field_fe.cc:754
VectorMPI::zero_entries
void zero_entries()
Definition: vector_mpi.hh:82
ComputeIntersection< 1, 3 >
Definition: compute_intersection.hh:343
ElementCacheMap
Directing class of FieldValueCache.
Definition: field_value_cache.hh:151
Input::Record::val
const Ret val(const string &key) const
Definition: accessors_impl.hh:31
ReaderCache::get_element_ids
static void get_element_ids(const FilePath &file_path, const Mesh &mesh)
Definition: reader_cache.cc:73
IntIdx
int IntIdx
Definition: index_types.hh:25
FEValueHandler< 0, spacedim, Value >::value_list
void value_list(const Armor::array &point_list, const ElementAccessor< spacedim > &elm, std::vector< typename Value::return_type > &value_list)
Returns std::vector of scalar values in several points at once.
Definition: fe_value_handler.cc:184
Input::Type::Selection::close
const Selection & close() const
Close the Selection, no more values can be added.
Definition: type_selection.cc:65
IntersectionLocal::compute_measure
double compute_measure() const override
Computes the relative measure of intersection object.
Definition: intersection_local.cc:52
FilePath
Dedicated class for storing path to input and output files.
Definition: file_path.hh:54
VectorMPI::resize
void resize(unsigned int local_size)
Definition: vector_mpi.cc:50
ElementDataCacheBase::n_comp
unsigned int n_comp() const
Definition: element_data_cache_base.hh:145
Input::Type::Double
Class for declaration of the input data that are floating point numbers.
Definition: type_base.hh:534
update_values
@ update_values
Shape function values.
Definition: update_flags.hh:87
MeshBase::undef_idx
static const unsigned int undef_idx
Definition: mesh.h:105
Quadrature::size
unsigned int size() const
Returns number of quadrature points.
Definition: quadrature.hh:86
FLOW123D_FORCE_LINK_IN_CHILD
#define FLOW123D_FORCE_LINK_IN_CHILD(x)
Definition: global_defs.h:104
THROW
#define THROW(whole_exception_expr)
Wrapper for throw. Saves the throwing point.
Definition: exceptions.hh:53
std::vector
Definition: doxy_dummy_defs.hh:7
MappingP1::project_real_to_unit
static BaryPoint project_real_to_unit(const RealPoint &point, const ElementMap &map)
Definition: mapping_p1.cc:69
ElementAccessor
Definition: dh_cell_accessor.hh:32
FieldFE::in_rec_
Input::Record in_rec_
Accessor to Input::Record.
Definition: field_fe.hh:297
FEValueHandler< 0, spacedim, Value >::set_boundary_dofs_vector
void set_boundary_dofs_vector(std::shared_ptr< std::vector< IntIdx > > boundary_dofs)
TODO: Temporary solution. Fix problem with merge new DOF handler and boundary Mesh....
Definition: fe_value_handler.hh:151
FieldFE::NativeFactory::dof_vector_
VectorMPI dof_vector_
Definition: field_fe.hh:110
reader_cache.hh
DHCellAccessor::dim
unsigned int dim() const
Return dimension of element appropriate to cell.
Definition: dh_cell_accessor.hh:101
FieldFE::local_to_ghost_data_scatter_begin
void local_to_ghost_data_scatter_begin()
Call begin scatter functions (local to ghost) on data vector.
Definition: field_fe.cc:872
field_fe.hh
VectorMPI::normalize
void normalize(unsigned int pos, double divisor)
Normalize value on given position.
Definition: vector_mpi.hh:118
FieldFE::boundary_domain_
bool boundary_domain_
Is set in set_mesh method. Value true means, that we accept only boundary element accessors in the va...
Definition: field_fe.hh:300
TimeStep::read_time
double read_time(Input::Iterator< Input::Tuple > time_it, double default_time=std::numeric_limits< double >::quiet_NaN()) const
Definition: time_governor.cc:262
ElementDataCacheBase::set_dof_handler_hash
void set_dof_handler_hash(std::size_t hash)
Definition: element_data_cache_base.hh:171
Input::Array::begin
Iterator< ValueType > begin() const
Definition: accessors_impl.hh:145
msh_gmshreader.h
ElementDataCacheBase::n_dofs_per_element
unsigned int n_dofs_per_element() const
Definition: element_data_cache_base.hh:152
fe_system.hh
Class FESystem for compound finite elements.
FieldFE::data_vec_
VectorMPI data_vec_
Store data of Field.
Definition: field_fe.hh:267
ASSERT_LT
#define ASSERT_LT(a, b)
Definition of comparative assert macro (Less Than) only for debug mode.
Definition: asserts.hh:300
Dim
Definition: mixed.hh:25
FieldFE::cache_reinit
void cache_reinit(const ElementCacheMap &cache_map) override
Definition: field_fe.cc:325
ElementCacheMap::eval_point_data
const EvalPointData & eval_point_data(unsigned int point_idx) const
Return item of eval_point_data_ specified by its position.
Definition: field_value_cache.hh:274
FEValueInitData::mixed_fe
MixedPtr< FiniteElement > mixed_fe
FiniteElement objects of all dimensions.
Definition: fe_value_handler.hh:50
fe_p.hh
Definitions of basic Lagrangean finite elements with polynomial shape functions.
BoundingBox
Bounding box in 3d ambient space.
Definition: bounding_box.hh:54
ComputeIntersection< 2, 3 >::init
void init()
Initializes lower dimensional objects. Sets correctly the pointers to Plucker coordinates and product...
Definition: compute_intersection.cc:1063
Armor::Array::n_rows
uint n_rows() const
Definition: armor.hh:715
FieldFE::init_from_input
virtual void init_from_input(const Input::Record &rec, const struct FieldAlgoBaseInitData &init_data)
Definition: field_fe.cc:348
VectorMPI::set
void set(unsigned int pos, double val)
Set value on given position.
Definition: vector_mpi.hh:111
FieldFE::fe_
MixedPtr< FiniteElement > fe_
Definition: field_fe.hh:317
ElementCacheMap::region_chunk_end
unsigned int region_chunk_end(unsigned int region_patch_idx) const
Return end position of region chunk in FieldValueCache.
Definition: field_value_cache.hh:257
FieldFE::dh_
std::shared_ptr< DOFHandlerMultiDim > dh_
DOF handler object.
Definition: field_fe.hh:265
Input::Type::Default
Class Input::Type::Default specifies default value of keys of a Input::Type::Record.
Definition: type_record.hh:61
Input::Type::Record::derive_from
virtual Record & derive_from(Abstract &parent)
Method to derive new Record from an AbstractRecord parent.
Definition: type_record.cc:196
FieldFE::NativeFactory::index_
unsigned int index_
Definition: field_fe.hh:108
FESystem::fe
const std::vector< std::shared_ptr< FiniteElement< dim > > > & fe() const
Definition: fe_system.hh:147
FieldFE::value
virtual const Value::return_type & value(const Point &p, const ElementAccessor< spacedim > &elm)
Definition: field_fe.cc:237
Mesh::bc_mesh
BCMesh * bc_mesh() const override
Implement MeshBase::bc_mesh(), getter of boundary mesh.
Definition: mesh.h:563
dh_cell_accessor.hh
FieldFE::get_interp_selection_input_type
static const Input::Type::Selection & get_interp_selection_input_type()
Definition: field_fe.cc:104
accessors.hh
FieldFE::set_mesh
void set_mesh(const Mesh *mesh, bool boundary_domain) override
Definition: field_fe.cc:371
TimeStep::end
double end() const
Definition: time_governor.hh:161
Input::Record
Accessor to the data with type Type::Record.
Definition: accessors.hh:291
FieldFE::default_value_
double default_value_
Default value of element if not set in mesh data file.
Definition: field_fe.hh:294
FieldFE::value_handler3_
FEValueHandler< 3, spacedim, Value > value_handler3_
Value handler that allows get value of 3D elements.
Definition: field_fe.hh:276
sys_profiler.hh
FEValueInitData::dh
std::shared_ptr< DOFHandlerMultiDim > dh
DOF handler object.
Definition: fe_value_handler.hh:38
ASSERT_PERMANENT
#define ASSERT_PERMANENT(expr)
Allow use shorter versions of macro names if these names is not used with external library.
Definition: asserts.hh:347
quadrature_lib.hh
Definitions of particular quadrature rules on simplices.
FieldAlgoBaseInitData
Helper struct stores data for initizalize descentants of FieldAlgorithmBase.
Definition: field_algo_base.hh:81
Quadrature::set
Armor::Array< double >::ArrayMatSet set(uint i)
Definition: quadrature.hh:97
TimeStep
Representation of one time step..
Definition: time_governor.hh:123
CheckResult
CheckResult
Return type of method that checked data stored in ElementDataCache (NaN values, limits)
Definition: element_data_cache.hh:36
FieldFE::vec
VectorMPI & vec()
Definition: field_fe.hh:181
ReaderCache::get_target_mesh_element_map
static std::shared_ptr< EquivalentMeshMap > get_target_mesh_element_map(const FilePath &file_path, Mesh *computational_mesh)
Definition: reader_cache.cc:79
ElementCacheMap::eval_points
std::shared_ptr< EvalPoints > eval_points() const
Getter of eval_points object.
Definition: field_value_cache.hh:193
Input::AbstractRecord
Accessor to the polymorphic input data of a type given by an AbstracRecord object.
Definition: accessors.hh:458
Input::Type::Default::obligatory
static Default obligatory()
The factory function to make an empty default value which is obligatory.
Definition: type_record.hh:110
FEValueHandler< 0, spacedim, Value >::value
const Value::return_type & value(const Point &p, const ElementAccessor< spacedim > &elm)
Returns one value in one given point.
Definition: fe_value_handler.hh:133
FieldCommon
Common abstract parent of all Field<...> classes.
Definition: field_common.hh:76
FETensor
@ FETensor
Definition: finite_element.hh:204
MappingP1::contains_point
static bool contains_point(arma::vec point, ElementAccessor< 3 > elm)
Test if element contains given point.
Definition: mapping_p1.cc:96
OutputTime
The class for outputting data during time.
Definition: output_time.hh:51
FEValueInitData::ndofs
unsigned int ndofs
number of dofs
Definition: fe_value_handler.hh:42
ASSERT_EQ
#define ASSERT_EQ(a, b)
Definition of comparative assert macro (EQual) only for debug mode.
Definition: asserts.hh:332
Input::Record::opt_val
bool opt_val(const string &key, Ret &value) const
Definition: accessors_impl.hh:107
Input::Type::Record::declare_key
Record & declare_key(const string &key, std::shared_ptr< TypeBase > type, const Default &default_value, const string &description, TypeBase::attribute_map key_attributes=TypeBase::attribute_map())
Declares a new key of the Record.
Definition: type_record.cc:503
FieldFE::interpolation_
DataInterpolation interpolation_
Specify type of FE data interpolation.
Definition: field_fe.hh:288
Input::Array::size
unsigned int size() const
Definition: accessors_impl.hh:163
mixed_fe_system
MixedPtr< FESystem > mixed_fe_system(MixedPtr< FiniteElement > fe, Args &&... args)
Definition: fe_system.hh:176
FieldFE::fe_item_
std::array< FEItem, 4 > fe_item_
Holds specific data of field evaluation over all dimensions.
Definition: field_fe.hh:316
FieldFE::discretization_
OutputTime::DiscreteSpace discretization_
Specify section where to find the field data in input mesh file.
Definition: field_fe.hh:285
ComputeIntersection< 1, 3 >::init
void init()
Initializes lower dimensional objects. Sets correctly the pointers to Plucker coordinates and product...
Definition: compute_intersection.cc:811
VectorMPI::local_to_ghost_begin
void local_to_ghost_begin()
local_to_ghost_{begin,end} updates the ghost values on neighbouring processors from local values
Definition: vector_mpi.hh:156
FEVector
@ FEVector
Definition: finite_element.hh:201
fmt::internal::isnan
DummyInt isnan(...)
Definition: format.h:306
FieldFE::interpolate_gauss
void interpolate_gauss(ElementDataCache< double >::CacheData data_vec)
Interpolate data (use Gaussian distribution) over all elements of target mesh.
Definition: field_fe.cc:558
Input::Type::Selection
Template for classes storing finite set of named values.
Definition: type_selection.hh:65
Input::Record::find
Iterator< Ret > find(const string &key) const
Definition: accessors_impl.hh:91
Armor::Array::n_cols
uint n_cols() const
Definition: armor.hh:720
FEValueHandler::compute_quadrature
unsigned int compute_quadrature(std::vector< arma::vec::fixed< 3 >> &q_points, std::vector< double > &q_weights, const ElementAccessor< spacedim > &elm, unsigned int order=3)
Compute real coordinates and weights (use QGauss) for given element.
Definition: fe_value_handler.cc:152
ElementAccessor::node
NodeAccessor< 3 > node(unsigned int ni) const
Definition: accessors.hh:230
Input::Type::FileName::input
static FileName input()
The factory function for declaring type FileName for input files.
Definition: type_base.cc:524
Armor::Array::set
ArrayMatSet set(uint index)
Definition: armor.hh:838
UnitConverter::get_input_type
static const Input::Type::Record & get_input_type()
Definition: unit_converter.cc:100
Input::Type::Record::close
Record & close() const
Close the Record for further declarations of keys.
Definition: type_record.cc:304
Armor::Array::size
unsigned int size() const
Definition: armor.hh:728
Input::Type
Definition: balance.hh:41
VectorMPI::add
void add(unsigned int pos, double val)
Add value to item on given position.
Definition: vector_mpi.hh:125
Input::Type::Record
Record type proxy class.
Definition: type_record.hh:182
FEValueInitData
Initialization structure of FEValueHandler class.
Definition: fe_value_handler.hh:35
ComputeIntersection< 1, 3 >::compute
unsigned int compute(std::vector< IPAux > &IP13s)
Computes intersection points for 1D-3D intersection. Computes lower dimensional CIs abscissa vs tetra...
Definition: compute_intersection.cc:833
FieldFE::calculate_identic_values
void calculate_identic_values(ElementDataCache< double >::CacheData data_cache)
Calculate data of identict_mesh interpolation on input data over all elements of target mesh.
Definition: field_fe.cc:783
QGauss
Symmetric Gauss-Legendre quadrature formulae on simplices.
Definition: quadrature_lib.hh:34
Value
@ Value
Definition: finite_element.hh:43
Field::FieldBasePtr
std::shared_ptr< FieldBaseType > FieldBasePtr
Definition: field.hh:96
FieldAlgoBaseInitData::flags_
FieldFlag::Flags flags_
Definition: field_algo_base.hh:95
not_a_number
@ not_a_number
Some value(s) is set to NaN.
Definition: element_data_cache.hh:39
intersection_aux.hh
Internal class representing intersection object.
FieldFE::native_data_to_cache
void native_data_to_cache(ElementDataCache< double > &output_data_cache)
Definition: field_fe.cc:846
LongIdx
int LongIdx
Define type that represents indices of large arrays (elements, nodes, dofs etc.)
Definition: index_types.hh:24
MappingP1::element_map
static ElementMap element_map(ElementAccessor< 3 > elm)
Definition: mapping_p1.cc:48
FEValueHandler< 0, spacedim, Value >::initialize
void initialize(FEValueInitData init_data)
Initialize data members.
Definition: fe_value_handler.cc:170
input_type.hh
FieldFE
Definition: field.hh:60
ElementCacheMap::region_chunk_begin
unsigned int region_chunk_begin(unsigned int region_patch_idx) const
Return begin position of region chunk in FieldValueCache.
Definition: field_value_cache.hh:251
Mesh
Definition: mesh.h:359
FieldFE::value_handler2_
FEValueHandler< 2, spacedim, Value > value_handler2_
Value handler that allows get value of 2D elements.
Definition: field_fe.hh:274
Input::Type::Record::copy_keys
Record & copy_keys(const Record &other)
Copy keys from other record.
Definition: type_record.cc:216
FieldAlgorithmBase
Definition: field_algo_base.hh:112
Input::Type::String
Class for declaration of the input data that are in string format.
Definition: type_base.hh:582
DHCellAccessor
Cell accessor allow iterate over DOF handler cells.
Definition: dh_cell_accessor.hh:43
FieldFE::set_fe_data
VectorMPI set_fe_data(std::shared_ptr< DOFHandlerMultiDim > dh, VectorMPI dof_values=VectorMPI::sequential(0), unsigned int block_index=FieldFE< spacedim, Value >::undef_uint)
Definition: field_fe.cc:173
Input::Array
Accessor to input data conforming to declared Array.
Definition: accessors.hh:566
ElementDataCache::CacheData
std::shared_ptr< std::vector< T > > CacheData
Definition: element_data_cache.hh:52
WarningOut
#define WarningOut()
Macro defining 'warning' record of log.
Definition: logger.hh:278
IntersectionAux
Internal auxiliary class representing intersection object of simplex<dimA> and simplex<dimB>.
Definition: compute_intersection.hh:47
INSTANCE_ALL
#define INSTANCE_ALL(field)
Definition: field_instances.hh:43
unit_converter.hh
Input::Tuple
Accessor to the data with type Type::Tuple.
Definition: accessors.hh:411
FieldFE::Point
FieldAlgorithmBase< spacedim, Value >::Point Point
Definition: field_fe.hh:53
fe_value_handler.hh
FieldFE::reader_file_
FilePath reader_file_
mesh reader file
Definition: field_fe.hh:279
ASSERT_LE
#define ASSERT_LE(a, b)
Definition of comparative assert macro (Less or Equal) only for debug mode.
Definition: asserts.hh:308
MeshBase
Base class for Mesh and BCMesh.
Definition: mesh.h:96
compute_intersection.hh
Fundamental simplicial intersections.
FEValueHandler::value
const Value::return_type & value(const Point &p, const ElementAccessor< spacedim > &elm)
Returns one value in one given point.
Definition: fe_value_handler.cc:108
field_instances.hh
BCMesh
Class represents boundary part of mesh.
Definition: bc_mesh.hh:37
FieldFlag::equation_input
static constexpr Mask equation_input
The field is data parameter of the owning equation. (default on)
Definition: field_flag.hh:33
MixedPtr< FiniteElement >
FieldFE::value_list
virtual void value_list(const Armor::array &point_list, const ElementAccessor< spacedim > &elm, std::vector< typename Value::return_type > &value_list)
Definition: field_fe.cc:261
IntersectionLocal< 1, 3 >
FieldCommon::get_flags
FieldFlag::Flags get_flags() const
Definition: field_common.hh:292
FieldFE::get_input_type
static const Input::Type::Record & get_input_type()
Implementation.
Definition: field_fe.cc:61
VectorMPI::local_to_ghost_end
void local_to_ghost_end()
local_to_ghost_{begin,end} updates the ghost values on neighbouring processors from local values
Definition: vector_mpi.hh:160
DHCellAccessor::get_loc_dof_indices
LocDofVec get_loc_dof_indices() const
Returns the local indices of dofs associated to the cell on the local process.
Definition: dh_cell_accessor.hh:88
ReaderCache::get_mesh
static std::shared_ptr< Mesh > get_mesh(const FilePath &file_path)
Definition: reader_cache.cc:40
ADD_CALLS
#define ADD_CALLS(n_calls)
Increase number of calls in actual timer.
Definition: sys_profiler.hh:186
Armor::Array< double >
FEValueInitData::data_vec
VectorMPI data_vec
Store data of Field.
Definition: fe_value_handler.hh:40
FieldFlag::declare_input
static constexpr Mask declare_input
The field can be set from input. The key in input field descriptor is declared. (default on)
Definition: field_flag.hh:35
FieldFE::fe_values_
std::vector< FEValues< spacedim > > fe_values_
List of FEValues objects of dimensions 0,1,2,3 used for value calculation.
Definition: field_fe.hh:310
VectorMPI::sequential
static VectorMPI sequential(unsigned int size)
Definition: vector_mpi.cc:44
FieldFE::get_disc_selection_input_type
static const Input::Type::Selection & get_disc_selection_input_type()
Definition: field_fe.cc:92
FieldCommon::n_comp
unsigned int n_comp() const
Definition: field_common.hh:271
ElementAccessor::idx
unsigned int idx() const
We need this method after replacing Region by RegionIdx, and movinf RegionDB instance into particular...
Definition: accessors.hh:215
FieldFE::interpolate_intersection
void interpolate_intersection(ElementDataCache< double >::CacheData data_vec)
Interpolate data (use intersection library) over all elements of target mesh.
Definition: field_fe.cc:652
FieldFE::set_time
bool set_time(const TimeStep &time) override
Definition: field_fe.cc:496
OutputTime::DiscreteSpace
DiscreteSpace
Definition: output_time.hh:108
DiscreteSpace
Definition: discrete_space.hh:41
mapping_p1.hh
Class MappingP1 implements the affine transformation of the unit cell onto the actual cell.
VectorMPI::get
double get(unsigned int pos) const
Return value on given position.
Definition: vector_mpi.hh:105
FEValueHandler::set_boundary_dofs_vector
void set_boundary_dofs_vector(std::shared_ptr< std::vector< IntIdx > > boundary_dofs)
TODO: Temporary solution. Fix problem with merge new DOF handler and boundary Mesh....
Definition: fe_value_handler.hh:80
ReaderCache::get_reader
static std::shared_ptr< BaseMeshReader > get_reader(const FilePath &file_path)
Definition: reader_cache.cc:36
FEValueHandler::value_list
void value_list(const Armor::array &point_list, const ElementAccessor< spacedim > &elm, std::vector< typename Value::return_type > &value_list)
Returns std::vector of scalar values in several points at once.
Definition: fe_value_handler.cc:121
TimeGovernor::get_input_time_type
static const Input::Type::Tuple & get_input_time_type(double lower_bound=-std::numeric_limits< double >::max(), double upper_bound=std::numeric_limits< double >::max())
Definition: time_governor.cc:47
FieldFE::fill_boundary_dofs
void fill_boundary_dofs()
Definition: field_fe.cc:406
FieldCommon::input_name
const std::string & input_name() const
Definition: field_common.hh:242
FEValueInitData::range_begin
unsigned int range_begin
Holds begin of component range of evaluation.
Definition: fe_value_handler.hh:46
FieldCommon::limits
std::pair< double, double > limits() const
Definition: field_common.hh:260
VectorMPI
Definition: vector_mpi.hh:43
FieldFE::NativeFactory::create_field
Field< spacedim, Value >::FieldBasePtr create_field(Input::Record rec, const FieldCommon &field) override
Definition: field_fe.cc:142
boundary
@ boundary
Definition: generic_assembly.hh:36
Input::Type::Selection::add_value
Selection & add_value(const int value, const std::string &key, const std::string &description="", TypeBase::attribute_map attributes=TypeBase::attribute_map())
Adds one new value with name given by key to the Selection.
Definition: type_selection.cc:50
FieldFE::~FieldFE
virtual ~FieldFE()
Destructor.
Definition: field_fe.cc:901
ASSERT_PTR
#define ASSERT_PTR(ptr)
Definition of assert macro checking non-null pointer (PTR) only for debug mode.
Definition: asserts.hh:340
Quadrature
Base class for quadrature rules on simplices in arbitrary dimensions.
Definition: quadrature.hh:48
FieldFE::make_dof_handler
void make_dof_handler(const MeshBase *mesh)
Create DofHandler object.
Definition: field_fe.cc:433
Input::Type::Default::optional
static Default optional()
The factory function to make an empty default value which is optional.
Definition: type_record.hh:124
Armor::ArmaMat
typename arma::Mat< Type >::template fixed< nr, nc > ArmaMat
Definition: armor.hh:502
START_TIMER
#define START_TIMER(tag)
Starts a timer with specified tag.
Definition: sys_profiler.hh:115
ComputeIntersection< 2, 3 >::compute
void compute(IntersectionAux< 2, 3 > &intersection)
Computes intersection points for 2D-3D intersection. Computes lower dimensional CIs: 1) 3x triangle s...
Definition: compute_intersection.cc:1130
FESystem
Compound finite element on dim dimensional simplex.
Definition: fe_system.hh:101
BaseMeshReader::HeaderQuery
Definition: msh_basereader.hh:136
ElementDataCache::store_value
void store_value(unsigned int idx, const T *value)
Definition: element_data_cache.cc:210
VectorMPI::size
unsigned int size() const
Return size of output data.
Definition: vector_mpi.hh:98
FieldFE::value_handler1_
FEValueHandler< 1, spacedim, Value > value_handler1_
Value handler that allows get value of 1D elements.
Definition: field_fe.hh:272
FieldFE::init_quad
Quadrature init_quad(std::shared_ptr< EvalPoints > eval_points)
Initialize FEValues object of given dimension.
Definition: field_fe.cc:338
END_TIMER
#define END_TIMER(tag)
Ends a timer with specified tag.
Definition: sys_profiler.hh:149
FEValueInitData::n_comp
unsigned int n_comp
number of components
Definition: fe_value_handler.hh:44
range_wrapper.hh
Implementation of range helper class.
intersection_local.hh
Classes with algorithms for computation of intersections of meshes.
FieldFE::calculate_equivalent_values
void calculate_equivalent_values(ElementDataCache< double >::CacheData data_cache)
Calculate data of equivalent_mesh interpolation on input over all elements of target mesh.
Definition: field_fe.cc:809