ProblemsManager

Adding and managing problems. More...

Collaboration diagram for ProblemsManager:

Files
file	ProblemsManager.cpp
	Managing complexities for problem.
file	ProblemsManager.hpp
	Interface for building, partitioning, and managing finite element problems.

Classes
struct	MoFEM::ProblemsManager
	Problem manager is used to build and partition problems. More...

Functions
MoFEMErrorCode	MoFEM::ProblemsManager::getOptions ()
	Get command line options for ProblemsManager.
DEPRECATED MoFEMErrorCode	MoFEM::ProblemsManager::partitionMesh (const Range &ents, const int dim, const int adj_dim, const int n_parts, Tag *th_vertex_weights=nullptr, Tag *th_edge_weights=nullptr, Tag *th_part_weights=nullptr, int verb=VERBOSE, const bool debug=false)
	Set partition tag to each finite element in the problem.
MoFEMErrorCode	MoFEM::ProblemsManager::buildProblem (const std::string name, const bool square_matrix, int verb=VERBOSE)
	build problem data structures
MoFEMErrorCode	MoFEM::ProblemsManager::buildProblem (Problem *problem_ptr, const bool square_matrix, int verb=VERBOSE)
	build problem data structures
MoFEMErrorCode	MoFEM::ProblemsManager::buildProblemOnDistributedMesh (const std::string name, const bool square_matrix, int verb=VERBOSE)
	build problem data structures, assuming that mesh is distributed (collective)
MoFEMErrorCode	MoFEM::ProblemsManager::buildProblemOnDistributedMesh (Problem *problem_ptr, const bool square_matrix=true, int verb=VERBOSE)
	build problem data structures, assuming that mesh is distributed (collective)
MoFEMErrorCode	MoFEM::ProblemsManager::buildSubProblem (const std::string out_name, const std::vector< std::string > &fields_row, const std::vector< std::string > &fields_col, const std::string main_problem, const bool square_matrix=true, const map< std::string, boost::shared_ptr< Range > > *entityMapRow=nullptr, const map< std::string, boost::shared_ptr< Range > > *entityMapCol=nullptr, int verb=VERBOSE)
	build sub problem
MoFEMErrorCode	MoFEM::ProblemsManager::buildComposedProblem (const std::string out_name, const std::vector< std::string > add_row_problems, const std::vector< std::string > add_col_problems, const bool square_matrix=true, int verb=1)
	build composite problem
MoFEMErrorCode	MoFEM::ProblemsManager::inheritPartition (const std::string name, const std::string problem_for_rows, bool copy_rows, const std::string problem_for_cols, bool copy_cols, int verb=VERBOSE)
	build indexing and partition problem inheriting indexing and partitioning from two other problems
MoFEMErrorCode	MoFEM::ProblemsManager::partitionSimpleProblem (const std::string name, int verb=VERBOSE)
	partition problem dofs
MoFEMErrorCode	MoFEM::ProblemsManager::partitionProblem (const std::string name, int verb=VERBOSE)
	partition problem dofs (collective)
MoFEMErrorCode	MoFEM::ProblemsManager::printPartitionedProblem (const Problem *problem_ptr, int verb=VERBOSE)
	Print partition information for debugging.
MoFEMErrorCode	MoFEM::ProblemsManager::debugPartitionedProblem (const Problem *problem_ptr, int verb=VERBOSE)
	Debug partition information.
MoFEMErrorCode	MoFEM::ProblemsManager::partitionFiniteElements (const std::string name, bool part_from_moab=false, int low_proc=-1, int hi_proc=-1, int verb=VERBOSE)
	partition finite elements
MoFEMErrorCode	MoFEM::ProblemsManager::partitionGhostDofs (const std::string name, int verb=VERBOSE)
	determine ghost nodes
MoFEMErrorCode	MoFEM::ProblemsManager::partitionGhostDofsOnDistributedMesh (const std::string name, int verb=VERBOSE)
	determine ghost nodes on distributed meshes
MoFEMErrorCode	MoFEM::ProblemsManager::getFEMeshset (const std::string prb_name, const std::string &fe_name, EntityHandle *meshset) const
	Create finite element meshset for the problem.
MoFEMErrorCode	MoFEM::ProblemsManager::getProblemElementsLayout (const std::string name, const std::string &fe_name, PetscLayout *layout) const
	Get layout of elements in the problem.
MoFEMErrorCode	MoFEM::ProblemsManager::removeDofsOnEntities (const std::string problem_name, const std::string field_name, const Range ents, const int lo_coeff=0, const int hi_coeff=MAX_DOFS_ON_ENTITY, const int lo_order=0, const int hi_order=100, int verb=VERBOSE, const bool debug=false)
	Remove DOFs from problem.
MoFEMErrorCode	MoFEM::ProblemsManager::removeDofsOnEntities (const std::string problem_name, const std::string field_name, const BitRefLevel bit_ref_level, const BitRefLevel bit_ref_mask, Range *ents_ptr=nullptr, const int lo_coeff=0, const int hi_coeff=MAX_DOFS_ON_ENTITY, const int lo_order=0, const int hi_order=100, int verb=VERBOSE, const bool debug=false)
	Remove DOFs from problem by bit ref level.
MoFEMErrorCode	MoFEM::ProblemsManager::removeDofs (const std::string problem_name, RowColData rc, std::vector< boost::weak_ptr< NumeredDofEntity > > &vec_dof_view, int verb=VERBOSE, const bool debug=false)
	Remove DOFs from problem on broken space.
MoFEMErrorCode	MoFEM::ProblemsManager::getSideDofsOnBrokenSpaceEntities (std::vector< boost::weak_ptr< NumeredDofEntity > > &vec_dof_view, const std::string problem_name, RowColData rc, const std::string field_name, const Range ents, int bridge_dim, const int lo_coeff=0, const int hi_coeff=MAX_DOFS_ON_ENTITY, const int lo_order=0, const int hi_order=100, int verb=VERBOSE, const bool debug=false) const
	Get DOFs on side entities for broken space.
MoFEMErrorCode	MoFEM::ProblemsManager::modifyMarkDofs (const std::string problem_name, RowColData rc, const std::string field_name, const int lo, const int hi, const enum MarkOP op, const unsigned char c, std::vector< unsigned char > &marker) const
	Modify DOF markers for specific field and coefficient range.
MoFEMErrorCode	MoFEM::ProblemsManager::markDofs (const std::string problem_name, RowColData rc, std::vector< boost::weak_ptr< NumeredDofEntity > > &vec_dof_view, const enum MarkOP op, std::vector< unsigned char > &marker) const
	Create vector with marked DOF indices based on DOF view.
MoFEMErrorCode	MoFEM::ProblemsManager::addFieldToEmptyFieldBlocks (const std::string problem_name, const std::string row_field, const std::string col_field) const
	Add empty field blocks to optimize matrix storage.

Read, load and broadcast
@
MoFEMErrorCode	MoFEM::CommInterface::partitionMesh (const Range &ents, const int dim, const int adj_dim, const int n_parts, Tag *th_vertex_weights=nullptr, Tag *th_edge_weights=nullptr, Tag *th_part_weights=nullptr, int verb=VERBOSE, const bool debug=false)
	Set partition tag to each finite element in the problem.

Detailed Description

Adding and managing problems.

Function Documentation

addFieldToEmptyFieldBlocks()

MoFEMErrorCode MoFEM::ProblemsManager::addFieldToEmptyFieldBlocks	(	const std::string	problem_name,
		const std::string	row_field,
		const std::string	col_field
	)		const

#include <src/interfaces/ProblemsManager.hpp>

Add empty field blocks to optimize matrix storage.

Marks field combinations as empty blocks in the matrix structure to optimize memory usage and computational efficiency. The MatrixManager assumes all field combinations result in non-zero blocks, but this allows specification of blocks that will remain zero for the entire problem duration.

Parameters

problem_name	name of the problem to modify
row_field	name of the field for matrix row blocks
col_field	name of the field for matrix column blocks

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 3696 of file ProblemsManager.cpp.

                                                                             {
 
  Interface &m_field = cOre;
  MoFEMFunctionBegin;
 
  const auto problem_ptr = m_field.get_problem(problem_name);
  auto get_field_id = [&](const std::string field_name) {
    return m_field.get_field_structure(field_name)->getId();
  };
  const auto row_id = get_field_id(row_field);
  const auto col_id = get_field_id(col_field);
 
  problem_ptr->addFieldToEmptyFieldBlocks(BlockFieldPair(row_id, col_id));
 
  MoFEMFunctionReturn(0);
}

buildComposedProblem()

MoFEMErrorCode MoFEM::ProblemsManager::buildComposedProblem	(	const std::string	out_name,
		const std::vector< std::string >	add_row_problems,
		const std::vector< std::string >	add_col_problems,
		const bool	square_matrix = true,
		int	verb = 1
	)

#include <src/interfaces/ProblemsManager.hpp>

build composite problem

Creates a composite problem by combining multiple existing problems. The resulting problem contains DOFs from all constituent problems, arranged in block matrix structure.

Parameters

out_name	name of the composite problem to create
add_row_problems	vector of problem names contributing to rows
add_col_problems	vector of problem names contributing to columns
square_matrix	true if the composite matrix is structurally symmetric
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 1246 of file ProblemsManager.cpp.

              {
  if (!(cOre.getBuildMoFEM() & Core::BUILD_FIELD))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "fields not build");
  if (!(cOre.getBuildMoFEM() & Core::BUILD_FE))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "FEs not build");
  if (!(cOre.getBuildMoFEM() & Core::BUILD_ADJ))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "adjacencies not build");
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  ProblemManagerFunctionBegin;
 
  CHKERR m_field.clear_problem(out_name);
  // get reference to all problems
  typedef Problem_multiIndex::index<Problem_mi_tag>::type ProblemByName;
  ProblemByName &problems_by_name =
      const_cast<ProblemByName &>(problems_ptr->get<Problem_mi_tag>());
 
  // Get iterators to out problem, i.e. build problem
  ProblemByName::iterator out_problem_it = problems_by_name.find(out_name);
  if (out_problem_it == problems_by_name.end()) {
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
             "problem with name < %s > not defined (top tip check spelling)",
             out_name.c_str());
  }
  // Make data structure for composed-problem data
  out_problem_it->composedProblemsData =
      boost::make_shared<ComposedProblemsData>();
  boost::shared_ptr<ComposedProblemsData> cmp_prb_data =
      out_problem_it->getComposedProblemsData();
 
  const std::vector<std::string> *add_prb[] = {&add_row_problems,
                                               &add_col_problems};
  std::vector<const Problem *> *add_prb_ptr[] = {&cmp_prb_data->rowProblemsAdd,
                                                 &cmp_prb_data->colProblemsAdd};
  std::vector<SmartPetscObj<IS>> *add_prb_is[] = {&cmp_prb_data->rowIs,
                                                  &cmp_prb_data->colIs};
 
  // Get local indices counter
  int *nb_local_dofs[] = {&out_problem_it->nbLocDofsRow,
                          &out_problem_it->nbLocDofsCol};
  // Get global indices counter
  int *nb_dofs[] = {&out_problem_it->nbDofsRow, &out_problem_it->nbDofsCol};
 
  // Set number of ghost nodes to zero
  {
    out_problem_it->nbDofsRow = 0;
    out_problem_it->nbDofsCol = 0;
    out_problem_it->nbLocDofsRow = 0;
    out_problem_it->nbLocDofsCol = 0;
    out_problem_it->nbGhostDofsRow = 0;
    out_problem_it->nbGhostDofsCol = 0;
  }
  int nb_dofs_reserve[] = {0, 0};
 
  // Loop over rows and columns in the main problem and sub-problems
  for (int ss = 0; ss != ((square_matrix) ? 1 : 2); ss++) {
    add_prb_ptr[ss]->reserve(add_prb[ss]->size());
    add_prb_is[ss]->reserve(add_prb[ss]->size());
    for (std::vector<std::string>::const_iterator vit = add_prb[ss]->begin();
         vit != add_prb[ss]->end(); vit++) {
      ProblemByName::iterator prb_it = problems_by_name.find(*vit);
      if (prb_it == problems_by_name.end()) {
        SETERRQ(
            PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
            "problem with name < %s > not defined (top tip check spelling)",
            vit->c_str());
      }
      add_prb_ptr[ss]->push_back(&*prb_it);
      // set number of dofs on rows and columns
      if (ss == 0) {
        // row
        *nb_dofs[ss] += add_prb_ptr[ss]->back()->getNbDofsRow();
        *nb_local_dofs[ss] += add_prb_ptr[ss]->back()->getNbLocalDofsRow();
        nb_dofs_reserve[ss] +=
            add_prb_ptr[ss]->back()->numeredRowDofsPtr->size();
      } else {
        // column
        *nb_dofs[ss] += add_prb_ptr[ss]->back()->getNbDofsCol();
        *nb_local_dofs[ss] += add_prb_ptr[ss]->back()->getNbLocalDofsCol();
        nb_dofs_reserve[ss] +=
            add_prb_ptr[ss]->back()->numeredColDofsPtr->size();
      }
    }
  }
  // if squre problem, rows and columns are the same
  if (square_matrix) {
    add_prb_ptr[1]->reserve(add_prb_ptr[0]->size());
    add_prb_is[1]->reserve(add_prb_ptr[0]->size());
    out_problem_it->numeredColDofsPtr = out_problem_it->numeredRowDofsPtr;
    *nb_dofs[1] = *nb_dofs[0];
    *nb_local_dofs[1] = *nb_local_dofs[0];
  }
 
  // reserve memory for dofs
  boost::shared_ptr<std::vector<NumeredDofEntity>> dofs_array[2];
  // Reserve memory
  for (int ss = 0; ss != ((square_matrix) ? 1 : 2); ss++) {
    dofs_array[ss] = boost::make_shared<std::vector<NumeredDofEntity>>();
    dofs_array[ss]->reserve(nb_dofs_reserve[ss]);
    if (!ss)
      out_problem_it->getRowDofsSequence()->emplace_back(dofs_array[ss]);
    else
      out_problem_it->getColDofsSequence()->emplace_back(dofs_array[ss]);
  }
 
  // Push back DOFs
  for (int ss = 0; ss != ((square_matrix) ? 1 : 2); ss++) {
    NumeredDofEntity_multiIndex::index<PetscGlobalIdx_mi_tag>::type::iterator
        dit,
        hi_dit;
    int shift_glob = 0;
    int shift_loc = 0;
    for (unsigned int pp = 0; pp != add_prb_ptr[ss]->size(); pp++) {
      PetscInt *dofs_out_idx_ptr;
      int nb_local_dofs = (*add_prb_ptr[ss])[pp]->getNbLocalDofsRow();
      CHKERR PetscMalloc(nb_local_dofs * sizeof(int), &dofs_out_idx_ptr);
      if (ss == 0) {
        dit = (*add_prb_ptr[ss])[pp]
                  ->numeredRowDofsPtr->get<PetscGlobalIdx_mi_tag>()
                  .begin();
        hi_dit = (*add_prb_ptr[ss])[pp]
                     ->numeredRowDofsPtr->get<PetscGlobalIdx_mi_tag>()
                     .end();
      } else {
        dit = (*add_prb_ptr[ss])[pp]
                  ->numeredColDofsPtr->get<PetscGlobalIdx_mi_tag>()
                  .begin();
        hi_dit = (*add_prb_ptr[ss])[pp]
                     ->numeredColDofsPtr->get<PetscGlobalIdx_mi_tag>()
                     .end();
      }
      int is_nb = 0;
      for (; dit != hi_dit; dit++) {
        const BitRefLevel &prb_bit = out_problem_it->getBitRefLevel();
        const BitRefLevel &prb_mask = out_problem_it->getBitRefLevelMask();
        const BitRefLevel &dof_bit = dit->get()->getBitRefLevel();
        if ((dof_bit & prb_bit).none() || ((dof_bit & prb_mask) != dof_bit))
          continue;
        const int rank = m_field.get_comm_rank();
        const int part = dit->get()->getPart();
        const int glob_idx = shift_glob + dit->get()->getPetscGlobalDofIdx();
        const int loc_idx =
            (part == rank) ? (shift_loc + dit->get()->getPetscLocalDofIdx())
                           : -1;
        dofs_array[ss]->emplace_back(dit->get()->getDofEntityPtr(), glob_idx,
                                     glob_idx, loc_idx, part);
        if (part == rank) {
          dofs_out_idx_ptr[is_nb++] = glob_idx;
        }
      }
      if (is_nb > nb_local_dofs) {
        SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                "Data inconsistency");
      }
      IS is;
      CHKERR ISCreateGeneral(m_field.get_comm(), is_nb, dofs_out_idx_ptr,
                             PETSC_OWN_POINTER, &is);
      auto smart_is = SmartPetscObj<IS>(is);
      (*add_prb_is[ss]).push_back(smart_is);
      if (ss == 0) {
        shift_glob += (*add_prb_ptr[ss])[pp]->getNbDofsRow();
        shift_loc += (*add_prb_ptr[ss])[pp]->getNbLocalDofsRow();
      } else {
        shift_glob += (*add_prb_ptr[ss])[pp]->getNbDofsCol();
        shift_loc += (*add_prb_ptr[ss])[pp]->getNbLocalDofsCol();
      }
      if (square_matrix) {
        (*add_prb_ptr[1]).push_back((*add_prb_ptr[0])[pp]);
        (*add_prb_is[1]).push_back(smart_is);
      }
    }
  }
 
  if ((*add_prb_is[1]).size() != (*add_prb_is[0]).size()) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY, "Data inconsistency");
  }
 
  // Insert DOFs to problem multi-index
  for (int ss = 0; ss != ((square_matrix) ? 1 : 2); ss++) {
    auto hint = (ss == 0) ? out_problem_it->numeredRowDofsPtr->end()
                          : out_problem_it->numeredColDofsPtr->end();
    for (auto &v : *dofs_array[ss])
      hint = (ss == 0) ? out_problem_it->numeredRowDofsPtr->emplace_hint(
                             hint, dofs_array[ss], &v)
                       : out_problem_it->numeredColDofsPtr->emplace_hint(
                             hint, dofs_array[ss], &v);
  }
 
  // Compress DOFs
  *nb_dofs[0] = 0;
  *nb_dofs[1] = 0;
  *nb_local_dofs[0] = 0;
  *nb_local_dofs[1] = 0;
  for (int ss = 0; ss != ((square_matrix) ? 1 : 2); ss++) {
 
    boost::shared_ptr<NumeredDofEntity_multiIndex> dofs_ptr;
    if (ss == 0) {
      dofs_ptr = out_problem_it->numeredRowDofsPtr;
    } else {
      dofs_ptr = out_problem_it->numeredColDofsPtr;
    }
    NumeredDofEntityByUId::iterator dit, hi_dit;
    dit = dofs_ptr->get<Unique_mi_tag>().begin();
    hi_dit = dofs_ptr->get<Unique_mi_tag>().end();
    std::vector<int> idx;
    idx.reserve(std::distance(dit, hi_dit));
    // set dofs in order entity and dof number on entity
    for (; dit != hi_dit; dit++) {
      if (dit->get()->getPart() == (unsigned int)m_field.get_comm_rank()) {
        bool success = dofs_ptr->get<Unique_mi_tag>().modify(
            dit, NumeredDofEntity_local_idx_change((*nb_local_dofs[ss])++));
        if (!success) {
          SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        }
        idx.push_back(dit->get()->getPetscGlobalDofIdx());
      } else {
        if (dit->get()->getPetscLocalDofIdx() != -1) {
          SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                  "local index should be negative");
        }
      }
    }
    if (square_matrix) {
      *nb_local_dofs[1] = *nb_local_dofs[0];
    }
 
    // set new dofs mapping
    IS is;
    CHKERR ISCreateGeneral(m_field.get_comm(), idx.size(), &*idx.begin(),
                           PETSC_USE_POINTER, &is);
    CHKERR ISGetSize(is, nb_dofs[ss]);
    if (square_matrix) {
      *nb_dofs[1] = *nb_dofs[0];
    }
 
    AO ao;
    CHKERR AOCreateMappingIS(is, PETSC_NULLPTR, &ao);
    for (unsigned int pp = 0; pp != (*add_prb_is[ss]).size(); pp++)
      CHKERR AOApplicationToPetscIS(ao, (*add_prb_is[ss])[pp]);
 
    // Set DOFs numeration
    {
      std::vector<int> idx_new;
      idx_new.reserve(dofs_ptr->size());
      for (NumeredDofEntityByUId::iterator dit =
               dofs_ptr->get<Unique_mi_tag>().begin();
           dit != dofs_ptr->get<Unique_mi_tag>().end(); dit++) {
        idx_new.push_back(dit->get()->getPetscGlobalDofIdx());
      }
      // set new global dofs numeration
      IS is_new;
      CHKERR ISCreateGeneral(m_field.get_comm(), idx_new.size(),
                             &*idx_new.begin(), PETSC_USE_POINTER, &is_new);
      CHKERR AOApplicationToPetscIS(ao, is_new);
      // set global indices to multi-index
      std::vector<int>::iterator vit = idx_new.begin();
      for (NumeredDofEntityByUId::iterator dit =
               dofs_ptr->get<Unique_mi_tag>().begin();
           dit != dofs_ptr->get<Unique_mi_tag>().end(); dit++) {
        bool success =
            dofs_ptr->modify(dit, NumeredDofEntity_part_and_glob_idx_change(
                                      dit->get()->getPart(), *(vit++)));
        if (!success) {
          SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        }
      }
      CHKERR ISDestroy(&is_new);
    }
    CHKERR ISDestroy(&is);
    CHKERR AODestroy(&ao);
  }
 
  CHKERR printPartitionedProblem(&*out_problem_it, verb);
  CHKERR debugPartitionedProblem(&*out_problem_it, verb);
 
  // Inidcate that porble has been build
  cOre.getBuildMoFEM() |= Core::BUILD_PROBLEM;
  cOre.getBuildMoFEM() |= Core::PARTITION_PROBLEM;
 
  MoFEMFunctionReturn(0);
}

buildProblem() [1/2]

MoFEMErrorCode MoFEM::ProblemsManager::buildProblem	(	const std::string	name,
		const bool	square_matrix,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

build problem data structures

Note

If square_matrix is set to true, that indicate that problem is structurally symmetric, i.e. rows and columns have the same dofs and are indexed in the same way.

Parameters

name	problem name
square_matrix	structurally symmetric problem
verb	verbosity level

Returns

error code

Examples

mofem/atom_tests/build_problems.cpp, mofem/atom_tests/continuity_check_on_contact_prism_side_ele.cpp, mofem/atom_tests/continuity_check_on_skeleton_3d.cpp, mofem/atom_tests/forces_and_sources_testing_edge_element.cpp, mofem/atom_tests/forces_and_sources_testing_flat_prism_element.cpp, mofem/atom_tests/hcurl_divergence_operator_2d.cpp, mofem/atom_tests/mesh_insert_interface_atom.cpp, mofem/atom_tests/prism_elements_from_surface.cpp, mofem/atom_tests/prism_polynomial_approximation.cpp, mofem/atom_tests/quad_polynomial_approximation.cpp, mofem/atom_tests/remove_entities_from_problem_not_partitioned.cpp, and mofem/users_modules/basic_finite_elements/nonlinear_elasticity/nonlinear_dynamics.cpp.

Definition at line 86 of file ProblemsManager.cpp.

                                                       {
 
  MoFEM::Interface &m_field = cOre;
  ProblemManagerFunctionBegin;
  if (!(cOre.getBuildMoFEM() & (1 << 0)))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "fields not build");
  if (!(cOre.getBuildMoFEM() & (1 << 1)))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "FEs not build");
  if (!(cOre.getBuildMoFEM() & (1 << 2)))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "adjacencies not build");
  const Problem *problem_ptr;
  CHKERR m_field.get_problem(name, &problem_ptr);
  CHKERR buildProblem(const_cast<Problem *>(problem_ptr), square_matrix, verb);
  cOre.getBuildMoFEM() |= 1 << 3; // It is assumed that user who uses this
                                  // function knows what he is doing
  MoFEMFunctionReturn(0);
}

buildProblem() [2/2]

MoFEMErrorCode MoFEM::ProblemsManager::buildProblem	(	Problem *	problem_ptr,
		const bool	square_matrix,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

build problem data structures

Note

If square_matrix is set to true, that indicate that problem is structurally symmetric, i.e. rows and columns have the same dofs and are indexed in the same way.

Parameters

problem	pointer
square_matrix	structurally symmetric problem
verb	verbosity level

Returns

error code

Definition at line 106 of file ProblemsManager.cpp.

                                                       {
  MoFEM::Interface &m_field = cOre;
  auto dofs_field_ptr = m_field.get_dofs();
  auto ents_field_ptr = m_field.get_field_ents();
  auto adjacencies_ptr = m_field.get_ents_elements_adjacency();
  ProblemManagerFunctionBegin;
  PetscLogEventBegin(MOFEM_EVENT_ProblemsManager, 0, 0, 0, 0);
 
  // Note: Only allowed changes on problem_ptr structure which not influence
  // multi-index.
 
  if (problem_ptr->getBitRefLevel().none()) {
    SETERRQ(PETSC_COMM_SELF, 1, "problem <%s> refinement level not set",
             problem_ptr->getName().c_str());
  }
  CHKERR m_field.clear_problem(problem_ptr->getName());
 
  // zero finite elements
  problem_ptr->numeredFiniteElementsPtr->clear();
 
  DofEntity_multiIndex_active_view dofs_rows, dofs_cols;
  auto make_rows_and_cols_view = [&](auto &dofs_rows, auto &dofs_cols) {
    MoFEMFunctionBeginHot;
    for (auto it = ents_field_ptr->begin(); it != ents_field_ptr->end(); ++it) {
 
      const auto uid = (*it)->getLocalUniqueId();
 
      auto r = adjacencies_ptr->get<Unique_mi_tag>().equal_range(uid);
      for (auto lo = r.first; lo != r.second; ++lo) {
 
        if ((lo->getBitFEId() & problem_ptr->getBitFEId()).any()) {
          std::array<bool, 2> row_col = {false, false};
 
          const BitRefLevel &prb_bit = problem_ptr->getBitRefLevel();
          const BitRefLevel &prb_mask = problem_ptr->getBitRefLevelMask();
          const BitRefLevel &fe_bit = lo->entFePtr->getBitRefLevel();
 
          // if entity is not problem refinement level
          if ((fe_bit & prb_mask) != fe_bit)
            continue;
          if ((fe_bit & prb_bit).none())
            continue;
 
          auto add_to_view = [&](auto &nb_dofs, auto &view, auto rc) {
            auto dit = nb_dofs->lower_bound(uid);
            decltype(dit) hi_dit;
            if (dit != nb_dofs->end()) {
              hi_dit = nb_dofs->upper_bound(
                  uid | static_cast<UId>(MAX_DOFS_ON_ENTITY - 1));
              view.insert(dit, hi_dit);
              row_col[rc] = true;
            }
          };
 
          if ((lo->entFePtr->getBitFieldIdRow() & (*it)->getId()).any())
            add_to_view(dofs_field_ptr, dofs_rows, ROW);
 
          if (!square_matrix)
            if ((lo->entFePtr->getBitFieldIdCol() & (*it)->getId()).any())
              add_to_view(dofs_field_ptr, dofs_cols, COL);
 
          if (square_matrix && row_col[ROW])
            break;
          else if (row_col[ROW] && row_col[COL])
            break;
        }
      }
    }
    MoFEMFunctionReturnHot(0);
  };
 
  CHKERR make_rows_and_cols_view(dofs_rows, dofs_cols);
 
  // Add row dofs to problem
  {
    // zero rows
    problem_ptr->nbDofsRow = 0;
    problem_ptr->nbLocDofsRow = 0;
    problem_ptr->nbGhostDofsRow = 0;
 
    // add dofs for rows
    DofEntity_multiIndex_active_view::nth_index<0>::type::iterator miit,
        hi_miit;
    hi_miit = dofs_rows.get<0>().end();
 
    int count_dofs = dofs_rows.get<1>().count(true);
    boost::shared_ptr<std::vector<NumeredDofEntity>> dofs_array =
        boost::shared_ptr<std::vector<NumeredDofEntity>>(
            new std::vector<NumeredDofEntity>());
    problem_ptr->getRowDofsSequence()->push_back(dofs_array);
    dofs_array->reserve(count_dofs);
    miit = dofs_rows.get<0>().begin();
    for (; miit != hi_miit; miit++) {
      if ((*miit)->getActive()) {
        dofs_array->emplace_back(*miit);
        dofs_array->back().dofIdx = (problem_ptr->nbDofsRow)++;
      }
    }
    auto hint = problem_ptr->numeredRowDofsPtr->end();
    for (auto &v : *dofs_array) {
      hint = problem_ptr->numeredRowDofsPtr->emplace_hint(hint, dofs_array, &v);
    }
  }
 
  // Add col dofs to problem
  if (!square_matrix) {
    // zero cols
    problem_ptr->nbDofsCol = 0;
    problem_ptr->nbLocDofsCol = 0;
    problem_ptr->nbGhostDofsCol = 0;
 
    // add dofs for cols
    DofEntity_multiIndex_active_view::nth_index<0>::type::iterator miit,
        hi_miit;
    hi_miit = dofs_cols.get<0>().end();
 
    int count_dofs = 0;
    miit = dofs_cols.get<0>().begin();
    for (; miit != hi_miit; miit++) {
      if (!(*miit)->getActive()) {
        continue;
      }
      count_dofs++;
    }
 
    boost::shared_ptr<std::vector<NumeredDofEntity>> dofs_array =
        boost::shared_ptr<std::vector<NumeredDofEntity>>(
            new std::vector<NumeredDofEntity>());
    problem_ptr->getColDofsSequence()->push_back(dofs_array);
    dofs_array->reserve(count_dofs);
    miit = dofs_cols.get<0>().begin();
    for (; miit != hi_miit; miit++) {
      if (!(*miit)->getActive()) {
        continue;
      }
      dofs_array->emplace_back(*miit);
      dofs_array->back().dofIdx = problem_ptr->nbDofsCol++;
    }
    auto hint = problem_ptr->numeredColDofsPtr->end();
    for (auto &v : *dofs_array) {
      hint = problem_ptr->numeredColDofsPtr->emplace_hint(hint, dofs_array, &v);
    }
  } else {
    problem_ptr->numeredColDofsPtr = problem_ptr->numeredRowDofsPtr;
    problem_ptr->nbLocDofsCol = problem_ptr->nbLocDofsRow;
    problem_ptr->nbDofsCol = problem_ptr->nbDofsRow;
  }
 
  // job done, some debugging and postprocessing
  if (verb >= VERBOSE) {
    MOFEM_LOG("SYNC", Sev::verbose)
        << problem_ptr->getName() << " Nb. local dofs "
        << problem_ptr->numeredRowDofsPtr->size() << " by "
        << problem_ptr->numeredColDofsPtr->size();
    MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::verbose);
  }
 
  if (verb >= NOISY) {
    MOFEM_LOG("SYNC", Sev::noisy)
        << "FEs row dofs " << *problem_ptr << " Nb. row dof "
        << problem_ptr->getNbDofsRow();
    for (auto &miit : *problem_ptr->numeredRowDofsPtr)
      MOFEM_LOG("SYNC", Sev::noisy) << *miit;
 
    MOFEM_LOG("SYNC", Sev::noisy)
        << "FEs col dofs " << *problem_ptr << " Nb. col dof "
        << problem_ptr->getNbDofsCol();
    for (auto &miit : *problem_ptr->numeredColDofsPtr)
      MOFEM_LOG("SYNC", Sev::noisy) << *miit;
    MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::noisy);
  }
 
  cOre.getBuildMoFEM() |= Core::BUILD_PROBLEM; // It is assumed that user who
                                               // uses this function knows
                                               // what he is doing
 
  PetscLogEventEnd(MOFEM_EVENT_ProblemsManager, 0, 0, 0, 0);
 
  MoFEMFunctionReturn(0);
}

buildProblemOnDistributedMesh() [1/2]

MoFEMErrorCode MoFEM::ProblemsManager::buildProblemOnDistributedMesh	(	const std::string	name,
		const bool	square_matrix,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

build problem data structures, assuming that mesh is distributed (collective)

Mesh is distributed, that means that each processor keeps only own part of the mesh and shared entities.

Collective - need to be run on all processors in communicator, i.e. each function has to call this function.

Parameters

name	problem name to build
square_matrix	true if problem has structurally symmetric matrix
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Examples

mofem/atom_tests/build_composite_problem.cpp, mofem/atom_tests/remove_entities_from_problem.cpp, and mofem/users_modules/basic_finite_elements/nonlinear_elasticity/nonlinear_dynamics.cpp.

Definition at line 289 of file ProblemsManager.cpp.

                                                              {
  MoFEM::Interface &m_field = cOre;
  ProblemManagerFunctionBegin;
 
  if (!((cOre.getBuildMoFEM()) & Core::BUILD_FIELD))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "fields not build");
  if (!((cOre.getBuildMoFEM()) & Core::BUILD_FE))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "FEs not build");
  if (!((cOre.getBuildMoFEM()) & Core::BUILD_ADJ))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "adjacencies not build");
 
  const Problem *problem_ptr;
  CHKERR m_field.get_problem(name, &problem_ptr);
  CHKERR buildProblemOnDistributedMesh(const_cast<Problem *>(problem_ptr),
                                       square_matrix, verb);
 
  cOre.getBuildMoFEM() |= Core::BUILD_PROBLEM;
  cOre.getBuildMoFEM() |= Core::PARTITION_PROBLEM;
 
  MoFEMFunctionReturn(0);
}

buildProblemOnDistributedMesh() [2/2]

MoFEMErrorCode MoFEM::ProblemsManager::buildProblemOnDistributedMesh	(	Problem *	problem_ptr,
		const bool	square_matrix = true,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

build problem data structures, assuming that mesh is distributed (collective)

Mesh is distributed, that means that each processor keeps only own part of the mesh and shared entities.

Collective - need to be run on all processors in communicator, i.e. each function has to call this function.

Parameters

problem_ptr	pointer to problem structure
square_matrix	true if problem has structurally symmetric matrix
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 312 of file ProblemsManager.cpp.

                                                              {
  MoFEM::Interface &m_field = cOre;
  auto fields_ptr = m_field.get_fields();
  auto fe_ptr = m_field.get_finite_elements();
  auto dofs_field_ptr = m_field.get_dofs();
  ProblemManagerFunctionBegin;
  PetscLogEventBegin(MOFEM_EVENT_ProblemsManager, 0, 0, 0, 0);
 
  // clear data structures
  CHKERR m_field.clear_problem(problem_ptr->getName());
 
  CHKERR getOptions();
 
  if (problem_ptr->getBitRefLevel().none())
    SETERRQ(PETSC_COMM_SELF, MOFEM_NOT_FOUND,
             "problem <%s> refinement level not set",
             problem_ptr->getName().c_str());
 
  int loop_size = 2;
  if (square_matrix) {
    loop_size = 1;
    problem_ptr->numeredColDofsPtr = problem_ptr->numeredRowDofsPtr;
  } else if (problem_ptr->numeredColDofsPtr == problem_ptr->numeredRowDofsPtr) {
    problem_ptr->numeredColDofsPtr =
        boost::shared_ptr<NumeredDofEntity_multiIndex>(
            new NumeredDofEntity_multiIndex());
  }
 
  const BitRefLevel &prb_bit = problem_ptr->getBitRefLevel();
  const BitRefLevel &prb_mask = problem_ptr->getBitRefLevelMask();
 
  // // get rows and cols dofs view based on data on elements
  DofEntity_multiIndex_active_view dofs_rows, dofs_cols;
 
  // Add DOFs to problem by visiting all elements and adding DOFs from
  // elements to the problem
  if (buildProblemFromFields == PETSC_FALSE) {
 
    auto make_rows_and_cols_view = [&](auto &dofs_rows, auto &dofs_cols) {
      auto ents_field_ptr = m_field.get_field_ents();
      auto adjacencies_ptr = m_field.get_ents_elements_adjacency();
      MoFEMFunctionBeginHot;
      for (auto it = ents_field_ptr->begin(); it != ents_field_ptr->end();
           ++it) {
 
        const auto uid = (*it)->getLocalUniqueId();
 
        auto r = adjacencies_ptr->get<Unique_mi_tag>().equal_range(uid);
        for (auto lo = r.first; lo != r.second; ++lo) {
 
          if ((lo->getBitFEId() & problem_ptr->getBitFEId()).any()) {
            std::array<bool, 2> row_col = {false, false};
 
            const BitRefLevel &fe_bit = lo->entFePtr->getBitRefLevel();
 
            // if entity is not problem refinement level
            if ((fe_bit & prb_bit).any() && (fe_bit & prb_mask) == fe_bit) {
 
              auto add_to_view = [&](auto dofs, auto &view, auto rc) {
                auto dit = dofs->lower_bound(uid);
                decltype(dit) hi_dit;
                if (dit != dofs->end()) {
                  hi_dit = dofs->upper_bound(
                      uid | static_cast<UId>(MAX_DOFS_ON_ENTITY - 1));
                  view.insert(dit, hi_dit);
                  row_col[rc] = true;
                }
              };
 
              if ((lo->entFePtr->getBitFieldIdRow() & (*it)->getId()).any())
                add_to_view(dofs_field_ptr, dofs_rows, ROW);
 
              if (!square_matrix)
                if ((lo->entFePtr->getBitFieldIdCol() & (*it)->getId()).any())
                  add_to_view(dofs_field_ptr, dofs_cols, COL);
 
              if (square_matrix && row_col[ROW])
                break;
              else if (row_col[ROW] && row_col[COL])
                break;
            }
          }
        }
      }
      MoFEMFunctionReturnHot(0);
    };
 
    CHKERR make_rows_and_cols_view(dofs_rows, dofs_cols);
  }
 
  // Add DOFS to the problem by searching all the filedes, and adding to
  // problem owned or shared DOFs
  if (buildProblemFromFields == PETSC_TRUE) {
    // Get fields IDs on elements
    BitFieldId fields_ids_row, fields_ids_col;
    for (auto fit = fe_ptr->begin(); fit != fe_ptr->end(); fit++) {
      if ((fit->get()->getId() & problem_ptr->getBitFEId()).any()) {
        fields_ids_row |= fit->get()->getBitFieldIdRow();
        fields_ids_col |= fit->get()->getBitFieldIdCol();
      }
    }
    // Get fields DOFs
    for (auto fit = fields_ptr->begin(); fit != fields_ptr->end(); fit++) {
      if ((fit->get()->getId() & (fields_ids_row | fields_ids_col)).any()) {
 
        auto dit = dofs_field_ptr->get<Unique_mi_tag>().lower_bound(
            FieldEntity::getLoBitNumberUId((*fit)->getBitNumber()));
        auto hi_dit = dofs_field_ptr->get<Unique_mi_tag>().upper_bound(
            FieldEntity::getHiBitNumberUId((*fit)->getBitNumber()));
 
        for (; dit != hi_dit; dit++) {
 
          const int owner_proc = dit->get()->getOwnerProc();
          if (owner_proc != m_field.get_comm_rank()) {
            const unsigned char pstatus = dit->get()->getPStatus();
            if (pstatus == 0) {
              continue;
            }
          }
 
          const auto &dof_bit = (*dit)->getBitRefLevel();
          // if entity is not problem refinement level
          if ((dof_bit & prb_bit).any() && (dof_bit & prb_mask) == dof_bit) {
 
            if ((fit->get()->getId() & fields_ids_row).any()) {
              dofs_rows.insert(*dit);
            }
            if (!square_matrix) {
              if ((fit->get()->getId() & fields_ids_col).any()) {
                dofs_cols.insert(*dit);
              }
            }
          }
        }
      }
    }
  }
 
  if (synchroniseProblemEntities) {
    // Get fields IDs on elements
    BitFieldId fields_ids_row, fields_ids_col;
    BitFieldId *fields_ids[2] = {&fields_ids_row, &fields_ids_col};
    for (FiniteElement_multiIndex::iterator fit = fe_ptr->begin();
         fit != fe_ptr->end(); fit++) {
      if ((fit->get()->getId() & problem_ptr->getBitFEId()).any()) {
        fields_ids_row |= fit->get()->getBitFieldIdRow();
        fields_ids_col |= fit->get()->getBitFieldIdCol();
      }
    }
 
    DofEntity_multiIndex_active_view *dofs_ptr[] = {&dofs_rows, &dofs_cols};
    for (int ss = 0; ss != ((square_matrix) ? 1 : 2); ++ss) {
      DofEntity_multiIndex_active_view::nth_index<1>::type::iterator miit,
          hi_miit;
      miit = dofs_ptr[ss]->get<1>().lower_bound(1);
      hi_miit = dofs_ptr[ss]->get<1>().upper_bound(1);
      Range ents_to_synchronise;
      for (; miit != hi_miit; ++miit) {
        if (miit->get()->getEntDofIdx() != 0)
          continue;
        ents_to_synchronise.insert(miit->get()->getEnt());
      }
      Range tmp_ents = ents_to_synchronise;
      CHKERR m_field.getInterface<CommInterface>()->synchroniseEntities(
          ents_to_synchronise, nullptr, verb);
      ents_to_synchronise = subtract(ents_to_synchronise, tmp_ents);
      for (auto fit = fields_ptr->begin(); fit != fields_ptr->end(); fit++) {
        if ((fit->get()->getId() & *fields_ids[ss]).any()) {
          const auto bit_number = (*fit)->getBitNumber();
          for (Range::pair_iterator pit = ents_to_synchronise.pair_begin();
               pit != ents_to_synchronise.pair_end(); ++pit) {
            const auto f = pit->first;
            const auto s = pit->second;
            const auto lo_uid =
                FieldEntity::getLocalUniqueIdCalculate(bit_number, f);
            const auto hi_uid =
                FieldEntity::getLocalUniqueIdCalculate(bit_number, s);
 
            auto dit = dofs_field_ptr->get<Unique_mi_tag>().lower_bound(lo_uid);
            auto hi_dit =
                dofs_field_ptr->get<Unique_mi_tag>().upper_bound(hi_uid);
 
            dofs_ptr[ss]->insert(dit, hi_dit);
          }
        }
      }
    }
  }
 
  // add dofs for rows and cols and set ownership
  DofEntity_multiIndex_active_view *dofs_ptr[] = {&dofs_rows, &dofs_cols};
  boost::shared_ptr<NumeredDofEntity_multiIndex> numered_dofs_ptr[] = {
      problem_ptr->numeredRowDofsPtr, problem_ptr->numeredColDofsPtr};
  int *nbdof_ptr[] = {&problem_ptr->nbDofsRow, &problem_ptr->nbDofsCol};
  int *local_nbdof_ptr[] = {&problem_ptr->nbLocDofsRow,
                            &problem_ptr->nbLocDofsCol};
  int *ghost_nbdof_ptr[] = {&problem_ptr->nbGhostDofsRow,
                            &problem_ptr->nbGhostDofsCol};
  for (int ss = 0; ss < 2; ss++) {
    *(nbdof_ptr[ss]) = 0;
    *(local_nbdof_ptr[ss]) = 0;
    *(ghost_nbdof_ptr[ss]) = 0;
  }
 
  // Loop over dofs on rows and columns and add to multi-indices in dofs
  // problem structure,  set partition for each dof
  int nb_local_dofs[] = {0, 0};
  for (int ss = 0; ss < loop_size; ss++) {
    DofEntity_multiIndex_active_view::nth_index<1>::type::iterator miit,
        hi_miit;
    miit = dofs_ptr[ss]->get<1>().lower_bound(1);
    hi_miit = dofs_ptr[ss]->get<1>().upper_bound(1);
    for (; miit != hi_miit; miit++) {
      int owner_proc = (*miit)->getOwnerProc();
      if (owner_proc == m_field.get_comm_rank()) {
        nb_local_dofs[ss]++;
      }
    }
  }
 
  // get layout
  int start_ranges[2], end_ranges[2];
  for (int ss = 0; ss != loop_size; ss++) {
    PetscLayout layout;
    CHKERR PetscLayoutCreate(m_field.get_comm(), &layout);
    CHKERR PetscLayoutSetBlockSize(layout, 1);
    CHKERR PetscLayoutSetLocalSize(layout, nb_local_dofs[ss]);
    CHKERR PetscLayoutSetUp(layout);
    CHKERR PetscLayoutGetSize(layout, &*nbdof_ptr[ss]);
    CHKERR PetscLayoutGetRange(layout, &start_ranges[ss], &end_ranges[ss]);
    CHKERR PetscLayoutDestroy(&layout);
  }
  if (square_matrix) {
    nbdof_ptr[1] = nbdof_ptr[0];
    nb_local_dofs[1] = nb_local_dofs[0];
    start_ranges[1] = start_ranges[0];
    end_ranges[1] = end_ranges[0];
  }
 
  // set local and global indices on own dofs
  const size_t idx_data_type_size = sizeof(IdxDataType);
  const size_t data_block_size = idx_data_type_size / sizeof(int);
 
  if (sizeof(IdxDataType) % sizeof(int)) {
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "data inconsistency");
  }
  std::vector<std::vector<IdxDataType>> ids_data_packed_rows(
      m_field.get_comm_size()),
      ids_data_packed_cols(m_field.get_comm_size());
 
  // Loop over dofs on this processor and prepare those dofs to send on
  // another proc
  for (int ss = 0; ss != loop_size; ++ss) {
 
    DofEntity_multiIndex_active_view::nth_index<0>::type::iterator miit,
        hi_miit;
    hi_miit = dofs_ptr[ss]->get<0>().end();
 
    boost::shared_ptr<std::vector<NumeredDofEntity>> dofs_array =
        boost::shared_ptr<std::vector<NumeredDofEntity>>(
            new std::vector<NumeredDofEntity>());
    int nb_dofs_to_add = 0;
    miit = dofs_ptr[ss]->get<0>().begin();
    for (; miit != hi_miit; ++miit) {
      // Only set global idx for dofs on this processor part
      if (!(miit->get()->getActive()))
        continue;
      ++nb_dofs_to_add;
    }
    dofs_array->reserve(nb_dofs_to_add);
    if (ss == 0) {
      problem_ptr->getRowDofsSequence()->push_back(dofs_array);
    } else {
      problem_ptr->getColDofsSequence()->push_back(dofs_array);
    }
 
    int &local_idx = *local_nbdof_ptr[ss];
    miit = dofs_ptr[ss]->get<0>().begin();
    for (; miit != hi_miit; ++miit) {
 
      // Only set global idx for dofs on this processor part
      if (!(miit->get()->getActive()))
        continue;
 
      dofs_array->emplace_back(*miit);
 
      int owner_proc = dofs_array->back().getOwnerProc();
      if (owner_proc < 0) {
        SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
                "data inconsistency");
      }
 
      if (owner_proc != m_field.get_comm_rank()) {
        dofs_array->back().pArt = owner_proc;
        dofs_array->back().dofIdx = -1;
        dofs_array->back().petscGloablDofIdx = -1;
        dofs_array->back().petscLocalDofIdx = -1;
      } else {
 
        // Set part and indexes
        int glob_idx = start_ranges[ss] + local_idx;
        dofs_array->back().pArt = owner_proc;
        dofs_array->back().dofIdx = glob_idx;
        dofs_array->back().petscGloablDofIdx = glob_idx;
        dofs_array->back().petscLocalDofIdx = local_idx;
        local_idx++;
 
        unsigned char pstatus = dofs_array->back().getPStatus();
        // check id dof is shared, if that is a case global idx added to data
        // structure and is sended to other processors
        if (pstatus > 0) {
 
          for (int proc = 0;
               proc < MAX_SHARING_PROCS &&
               -1 != dofs_array->back().getSharingProcsPtr()[proc];
               proc++) {
            // make it different for rows and columns when needed
            if (ss == 0) {
              ids_data_packed_rows[dofs_array->back()
                                       .getSharingProcsPtr()[proc]]
                  .emplace_back(dofs_array->back().getGlobalUniqueId(),
                                glob_idx);
            } else {
              ids_data_packed_cols[dofs_array->back()
                                       .getSharingProcsPtr()[proc]]
                  .emplace_back(dofs_array->back().getGlobalUniqueId(),
                                glob_idx);
            }
            if (!(pstatus & PSTATUS_MULTISHARED)) {
              break;
            }
          }
        }
      }
    }
 
    auto hint = numered_dofs_ptr[ss]->end();
    for (auto &v : *dofs_array)
      hint = numered_dofs_ptr[ss]->emplace_hint(hint, dofs_array, &v);
  }
  if (square_matrix) {
    local_nbdof_ptr[1] = local_nbdof_ptr[0];
  }
 
  int nsends_rows = 0, nsends_cols = 0;
  // Non zero lengths[i] represent a message to i of length lengths[i].
  std::vector<int> lengths_rows(m_field.get_comm_size()),
      lengths_cols(m_field.get_comm_size());
  lengths_rows.clear();
  lengths_cols.clear();
  for (int proc = 0; proc < m_field.get_comm_size(); proc++) {
    lengths_rows[proc] = ids_data_packed_rows[proc].size() * data_block_size;
    lengths_cols[proc] = ids_data_packed_cols[proc].size() * data_block_size;
    if (!ids_data_packed_rows[proc].empty())
      nsends_rows++;
    if (!ids_data_packed_cols[proc].empty())
      nsends_cols++;
  }
 
  MPI_Status *status;
  CHKERR PetscMalloc1(m_field.get_comm_size(), &status);
 
  // Do rows
  int nrecvs_rows;    // number of messages received
  int *onodes_rows;   // list of node-ids from which messages are expected
  int *olengths_rows; // corresponding message lengths
  int **rbuf_row;     // must bee freed by user
 
  // make sure it is a PETSc comm
  MPI_Comm comm;
  CHKERR PetscCommDuplicate(m_field.get_comm(), &comm, NULL);
 
  {
 
    // rows
 
    // Computes the number of messages a node expects to receive
    CHKERR PetscGatherNumberOfMessages(comm, NULL, &lengths_rows[0],
                                       &nrecvs_rows);
    // std::cerr << nrecvs_rows << std::endl;
 
    // Computes info about messages that a MPI-node will receive, including
    // (from-id,length) pairs for each message.
    CHKERR PetscGatherMessageLengths(comm, nsends_rows, nrecvs_rows,
                                     &lengths_rows[0], &onodes_rows,
                                     &olengths_rows);
 
    // Gets a unique new tag from a PETSc communicator. All processors that
    // share the communicator MUST call this routine EXACTLY the same number
    // of times. This tag should only be used with the current objects
    // communicator; do NOT use it with any other MPI communicator.
    int tag_row;
    CHKERR PetscCommGetNewTag(comm, &tag_row);
 
    // Allocate a buffer sufficient to hold messages of size specified in
    // olengths. And post Irecvs on these buffers using node info from onodes
    MPI_Request *r_waits_row; // must bee freed by user
    // rbuf has a pointers to messeges. It has size of of nrecvs (number of
    // messages) +1. In the first index a block is allocated,
    // such that rbuf[i] = rbuf[i-1]+olengths[i-1].
 
    CHKERR PetscPostIrecvInt(comm, tag_row, nrecvs_rows, onodes_rows,
                             olengths_rows, &rbuf_row, &r_waits_row);
    CHKERR PetscFree(onodes_rows);
 
    MPI_Request *s_waits_row; // status of sens messages
    CHKERR PetscMalloc1(nsends_rows, &s_waits_row);
 
    // Send messeges
    for (int proc = 0, kk = 0; proc < m_field.get_comm_size(); proc++) {
      if (!lengths_rows[proc])
        continue; // no message to send to this proc
      CHKERR MPI_Isend(&(ids_data_packed_rows[proc])[0], // buffer to send
                       lengths_rows[proc],               // message length
                       MPIU_INT, proc,                   // to proc
                       tag_row, comm, s_waits_row + kk);
      kk++;
    }
 
    if (nrecvs_rows) {
      CHKERR MPI_Waitall(nrecvs_rows, r_waits_row, status);
    }
    if (nsends_rows) {
      CHKERR MPI_Waitall(nsends_rows, s_waits_row, status);
    }
 
    CHKERR PetscFree(r_waits_row);
    CHKERR PetscFree(s_waits_row);
  }
 
  // cols
  int nrecvs_cols = nrecvs_rows;
  int *olengths_cols = olengths_rows;
  PetscInt **rbuf_col = rbuf_row;
  if (!square_matrix) {
 
    // Computes the number of messages a node expects to receive
    CHKERR PetscGatherNumberOfMessages(comm, NULL, &lengths_cols[0],
                                       &nrecvs_cols);
 
    // Computes info about messages that a MPI-node will receive, including
    // (from-id,length) pairs for each message.
    int *onodes_cols;
    CHKERR PetscGatherMessageLengths(comm, nsends_cols, nrecvs_cols,
                                     &lengths_cols[0], &onodes_cols,
                                     &olengths_cols);
 
    // Gets a unique new tag from a PETSc communicator.
    int tag_col;
    CHKERR PetscCommGetNewTag(comm, &tag_col);
 
    // Allocate a buffer sufficient to hold messages of size specified in
    // olengths. And post Irecvs on these buffers using node info from onodes
    MPI_Request *r_waits_col; // must bee freed by user
    CHKERR PetscPostIrecvInt(comm, tag_col, nrecvs_cols, onodes_cols,
                             olengths_cols, &rbuf_col, &r_waits_col);
    CHKERR PetscFree(onodes_cols);
 
    MPI_Request *s_waits_col; // status of sens messages
    CHKERR PetscMalloc1(nsends_cols, &s_waits_col);
 
    // Send messages
    for (int proc = 0, kk = 0; proc < m_field.get_comm_size(); proc++) {
      if (!lengths_cols[proc])
        continue; // no message to send to this proc
      CHKERR MPI_Isend(&(ids_data_packed_cols[proc])[0], // buffer to send
                       lengths_cols[proc],               // message length
                       MPIU_INT, proc,                   // to proc
                       tag_col, comm, s_waits_col + kk);
      kk++;
    }
 
    if (nrecvs_cols) {
      CHKERR MPI_Waitall(nrecvs_cols, r_waits_col, status);
    }
    if (nsends_cols) {
      CHKERR MPI_Waitall(nsends_cols, s_waits_col, status);
    }
 
    CHKERR PetscFree(r_waits_col);
    CHKERR PetscFree(s_waits_col);
  }
 
  CHKERR PetscCommDestroy(&comm);
  CHKERR PetscFree(status);
 
  DofEntity_multiIndex_global_uid_view dofs_glob_uid_view;
  auto hint = dofs_glob_uid_view.begin();
  for (auto dof : *m_field.get_dofs())
    dofs_glob_uid_view.emplace_hint(hint, dof);
 
  // set values received from other processors
  for (int ss = 0; ss != loop_size; ++ss) {
 
    int nrecvs;
    int *olengths;
    int **data_procs;
    if (ss == 0) {
      nrecvs = nrecvs_rows;
      olengths = olengths_rows;
      data_procs = rbuf_row;
    } else {
      nrecvs = nrecvs_cols;
      olengths = olengths_cols;
      data_procs = rbuf_col;
    }
 
    UId uid;
    for (int kk = 0; kk != nrecvs; ++kk) {
      int len = olengths[kk];
      int *data_from_proc = data_procs[kk];
      for (int dd = 0; dd < len; dd += data_block_size) {
        uid = IdxDataTypePtr(&data_from_proc[dd]).getUId();
        auto ddit = dofs_glob_uid_view.find(uid);
        const auto owner_proc = FieldEntity::getOwnerFromUniqueId(uid);
 
        if (owner_proc == m_field.get_comm_rank() &&
            PetscUnlikely(ddit == dofs_glob_uid_view.end())) {
 
#ifndef NDEBUG
          auto ents_field_ptr = m_field.get_field_ents();
          MOFEM_LOG("SELF", Sev::error)
              << "DOF is shared or multishared between processors. For example "
                 "if order of field on given entity is set in inconsistently, "
                 "has different value on two processor, error such as this is "
                 "triggered";
 
          MOFEM_LOG("SELF", Sev::error) << "UId " << uid << " is not found";
          MOFEM_LOG("SELF", Sev::error)
              << "Problematic UId owner proc is " << owner_proc;
          const auto uid_handle = FieldEntity::getHandleFromUniqueId(uid);
          MOFEM_LOG("SELF", Sev::error)
              << "Problematic UId entity owning processor handle is "
              << uid_handle << " entity type "
              << moab::CN::EntityTypeName(type_from_handle(uid_handle));
          const auto uid_bit_number =
              FieldEntity::getFieldBitNumberFromUniqueId(uid);
          MOFEM_LOG("SELF", Sev::error)
              << "Problematic UId field is "
              << m_field.get_field_name(
                     field_bit_from_bit_number(uid_bit_number));
 
          FieldEntity_multiIndex_global_uid_view field_view;
          field_view.insert(ents_field_ptr->begin(), ents_field_ptr->end());
          auto fe_it = field_view.find(FieldEntity::getGlobalUniqueIdCalculate(
              owner_proc, uid_bit_number, uid_handle));
          if (fe_it == field_view.end()) {
            MOFEM_LOG("SELF", Sev::error)
                << "Also, no field entity in database for given global UId";
          } else {
            MOFEM_LOG("SELF", Sev::error) << "Field entity in databse exist "
                                             "(but have no DOF wih give UId";
            MOFEM_LOG("SELF", Sev::error) << **fe_it;
 
            // Save file with missing entity
            auto error_file_name =
                "error_with_missing_entity_" +
                boost::lexical_cast<std::string>(m_field.get_comm_rank()) +
                ".vtk";
            MOFEM_LOG("SELF", Sev::error)
                << "Look to file < " << error_file_name
                << " > it contains entity with missing DOF.";
 
            auto tmp_msh = get_temp_meshset_ptr(m_field.get_moab());
            const auto local_fe_ent = (*fe_it)->getEnt();
            CHKERR m_field.get_moab().add_entities(*tmp_msh, &local_fe_ent, 1);
            CHKERR m_field.get_moab().write_file(error_file_name.c_str(), "VTK",
                                                 "", tmp_msh->get_ptr(), 1);
          }
#endif
 
          SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                  "DOF with global UId not found (Compile code in Debug to "
                  "learn more about problem");
        }
 
        if (PetscUnlikely(ddit == dofs_glob_uid_view.end())) {
          continue;
        }
 
        auto dit = numered_dofs_ptr[ss]->find((*ddit)->getLocalUniqueId());
 
        if (dit != numered_dofs_ptr[ss]->end()) {
 
          int global_idx = IdxDataTypePtr(&data_from_proc[dd]).getDofIdx();
#ifndef NDEBUG
          if (PetscUnlikely(global_idx < 0))
            SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                    "received negative dof");
#endif
          bool success;
          success = numered_dofs_ptr[ss]->modify(
              dit, NumeredDofEntity_mofem_index_change(global_idx));
 
#ifndef NDEBUG
          if (PetscUnlikely(!success))
            SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
#endif
          success = numered_dofs_ptr[ss]->modify(
              dit, NumeredDofEntity_part_and_glob_idx_change((*dit)->getPart(),
                                                             global_idx));
#ifndef NDEBUG
          if (PetscUnlikely(!success))
            SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
#endif
        };
 
#ifndef NDEBUG
        if (PetscUnlikely(ddit->get()->getPStatus() == 0)) {
 
          // Dof is shared on this processor, however there is no element
          // which have this dof. If DOF is not shared and received from other
          // processor, but not marked as a shared on other that means that is
          // data inconstancy and error should be thrown.
 
          std::ostringstream zz;
          zz << **ddit << std::endl;
          SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                   "data inconsistency, dofs is not shared, but received "
                   "from other proc\n"
                   "%s",
                   zz.str().c_str());
        }
#endif
      }
    }
  }
 
  if (square_matrix) {
    (problem_ptr->nbDofsCol) = (problem_ptr->nbDofsRow);
    (problem_ptr->nbLocDofsCol) = (problem_ptr->nbLocDofsRow);
  }
 
  CHKERR PetscFree(olengths_rows);
  CHKERR PetscFree(rbuf_row[0]);
  CHKERR PetscFree(rbuf_row);
  if (!square_matrix) {
    CHKERR PetscFree(olengths_cols);
    CHKERR PetscFree(rbuf_col[0]);
    CHKERR PetscFree(rbuf_col);
  }
 
  if (square_matrix) {
    if (numered_dofs_ptr[0]->size() != numered_dofs_ptr[1]->size()) {
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
              "data inconsistency for square_matrix %ld!=%ld",
              numered_dofs_ptr[0]->size(), numered_dofs_ptr[1]->size());
    }
    if (problem_ptr->numeredRowDofsPtr != problem_ptr->numeredColDofsPtr) {
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
              "data inconsistency for square_matrix");
    }
  }
 
  CHKERR printPartitionedProblem(problem_ptr, verb);
  CHKERR debugPartitionedProblem(problem_ptr, verb);
 
  PetscLogEventEnd(MOFEM_EVENT_ProblemsManager, 0, 0, 0, 0);
 
  MoFEMFunctionReturn(0);
}

buildSubProblem()

MoFEMErrorCode MoFEM::ProblemsManager::buildSubProblem	(	const std::string	out_name,
		const std::vector< std::string > &	fields_row,
		const std::vector< std::string > &	fields_col,
		const std::string	main_problem,
		const bool	square_matrix = true,
		const map< std::string, boost::shared_ptr< Range > > *	entityMapRow = nullptr,
		const map< std::string, boost::shared_ptr< Range > > *	entityMapCol = nullptr,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

build sub problem

Creates a sub-problem from a main problem by selecting specific fields for rows and columns. This is useful for creating focused problems that operate on subsets of the full problem's fields.

Parameters

out_name	name of the output sub-problem to create
fields_row	vector of field names for problem rows
fields_col	vector of field names for problem columns
main_problem	name of the main problem to extract from
square_matrix	true if the sub-problem matrix is structurally symmetric
entityMapRow	optional map restricting row fields to specific entities
entityMapCol	optional map restricting column fields to specific entities
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Examples

mofem/atom_tests/remove_entities_from_problem.cpp, and mofem/tutorials/vec-5/free_surface.cpp.

Definition at line 977 of file ProblemsManager.cpp.

              {
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  ProblemManagerFunctionBegin;
 
  CHKERR m_field.clear_problem(out_name);
 
  // get reference to all problems
  using ProblemByName = decltype(problems_ptr->get<Problem_mi_tag>());
  auto &problems_by_name =
      const_cast<ProblemByName &>(problems_ptr->get<Problem_mi_tag>());
 
  // get iterators to out problem, i.e. build problem
  auto out_problem_it = problems_by_name.find(out_name);
  if (out_problem_it == problems_by_name.end()) {
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
             "subproblem with name < %s > not defined (top tip check spelling)",
             out_name.c_str());
  }
  // get iterator to main problem, i.e. out problem is subproblem of main
  // problem
  auto main_problem_it = problems_by_name.find(main_problem);
  if (main_problem_it == problems_by_name.end()) {
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
             "problem of subproblem with name < %s > not defined (top tip "
             "check spelling)",
             main_problem.c_str());
  }
 
  // get dofs for row & columns for out problem,
  boost::shared_ptr<NumeredDofEntity_multiIndex> out_problem_dofs[] = {
      out_problem_it->numeredRowDofsPtr, out_problem_it->numeredColDofsPtr};
  // get dofs for row & columns for main problem
  boost::shared_ptr<NumeredDofEntity_multiIndex> main_problem_dofs[] = {
      main_problem_it->numeredRowDofsPtr, main_problem_it->numeredColDofsPtr};
  // get local indices counter
  int *nb_local_dofs[] = {&out_problem_it->nbLocDofsRow,
                          &out_problem_it->nbLocDofsCol};
  // get global indices counter
  int *nb_dofs[] = {&out_problem_it->nbDofsRow, &out_problem_it->nbDofsCol};
 
  // set number of ghost nodes to zero
  {
    out_problem_it->nbGhostDofsRow = 0;
    out_problem_it->nbGhostDofsCol = 0;
  }
 
  // put rows & columns field names in array
  std::vector<std::string> fields[] = {fields_row, fields_col};
  const map<std::string, boost::shared_ptr<Range>> *entityMap[] = {
      entityMapRow, entityMapCol};
 
  // make data structure fos sub-problem data
  out_problem_it->subProblemData =
      boost::make_shared<Problem::SubProblemData>();
 
  // Loop over rows and columns
  for (int ss = 0; ss != (square_matrix ? 1 : 2); ++ss) {
 
    // reset dofs and columns counters
    (*nb_local_dofs[ss]) = 0;
    (*nb_dofs[ss]) = 0;
    // clear arrays
    out_problem_dofs[ss]->clear();
 
    // If DOFs are cleared clear finite elements too.
    out_problem_it->numeredFiniteElementsPtr->clear();
 
    // get dofs by field name and insert them in out problem multi-indices
    for (auto field : fields[ss]) {
 
      // Following reserve memory in sequences, only two allocations are here,
      // once for array of objects, next for array of shared pointers
 
      // aliased sequence of pointer is killed with element
      boost::shared_ptr<std::vector<NumeredDofEntity>> dofs_array =
          boost::make_shared<std::vector<NumeredDofEntity>>();
      // reserve memory for field  dofs
      if (!ss)
        out_problem_it->getRowDofsSequence()->emplace_back(dofs_array);
      else
        out_problem_it->getColDofsSequence()->emplace_back(dofs_array);
 
      // create elements objects
      auto bit_number = m_field.get_field_bit_number(field);
 
      auto add_dit_to_dofs_array = [&](auto &dit) {
        if (dit->get()->getPetscGlobalDofIdx() >= 0)
          dofs_array->emplace_back(
              dit->get()->getDofEntityPtr(), dit->get()->getPetscGlobalDofIdx(),
              dit->get()->getPetscGlobalDofIdx(),
              dit->get()->getPetscLocalDofIdx(), dit->get()->getPart());
      };
 
      auto get_dafult_dof_range = [&]() {
        auto dit = main_problem_dofs[ss]->get<Unique_mi_tag>().lower_bound(
            FieldEntity::getLoBitNumberUId(bit_number));
        auto hi_dit = main_problem_dofs[ss]->get<Unique_mi_tag>().upper_bound(
            FieldEntity::getHiBitNumberUId(bit_number));
        return std::make_pair(dit, hi_dit);
      };
 
      auto check = [&](auto &field) -> boost::shared_ptr<Range> {
        if (entityMap[ss]) {
          auto mit = entityMap[ss]->find(field);
          if (mit != entityMap[ss]->end()) {
            return mit->second;
          } else {
            return nullptr;
          }
        } else {
          return nullptr;
        }
      };
 
      if (auto r_ptr = check(field)) {
        for (auto p = r_ptr->pair_begin(); p != r_ptr->pair_end(); ++p) {
          const auto lo_ent = p->first;
          const auto hi_ent = p->second;
          auto dit = main_problem_dofs[ss]->get<Unique_mi_tag>().lower_bound(
              DofEntity::getLoFieldEntityUId(bit_number, lo_ent));
          auto hi_dit = main_problem_dofs[ss]->get<Unique_mi_tag>().upper_bound(
              DofEntity::getHiFieldEntityUId(bit_number, hi_ent));
          dofs_array->reserve(std::distance(dit, hi_dit));
          for (; dit != hi_dit; dit++) {
            add_dit_to_dofs_array(dit);
          }
        }
      } else {
        auto [dit, hi_dit] = get_dafult_dof_range();
        dofs_array->reserve(std::distance(dit, hi_dit));
        for (; dit != hi_dit; dit++)
          add_dit_to_dofs_array(dit);
      }
 
      // fill multi-index
      auto hint = out_problem_dofs[ss]->end();
      for (auto &v : *dofs_array)
        hint = out_problem_dofs[ss]->emplace_hint(hint, dofs_array, &v);
    }
    // Set local indexes
    {
      auto dit = out_problem_dofs[ss]->get<Idx_mi_tag>().begin();
      auto hi_dit = out_problem_dofs[ss]->get<Idx_mi_tag>().end();
      for (; dit != hi_dit; dit++) {
        int idx = -1; // if dof is not part of partition, set local index to -1
        if (dit->get()->getPart() == (unsigned int)m_field.get_comm_rank()) {
          idx = (*nb_local_dofs[ss])++;
        }
        bool success = out_problem_dofs[ss]->modify(
            out_problem_dofs[ss]->project<0>(dit),
            NumeredDofEntity_local_idx_change(idx));
        if (!success) {
          SETERRQ(PETSC_COMM_WORLD, MOFEM_ATOM_TEST_INVALID,
                  "operation unsuccessful");
        }
      };
    }
    // Set global indexes, compress global indices
    {
      auto dit =
          out_problem_dofs[ss]->get<PetscLocalIdx_mi_tag>().lower_bound(0);
      auto hi_dit =
          out_problem_dofs[ss]->get<PetscLocalIdx_mi_tag>().upper_bound(
              out_problem_dofs[ss]->size());
      const int nb = std::distance(dit, hi_dit);
      // get main problem global indices
      std::vector<int> main_indices(nb);
      for (auto it = main_indices.begin(); dit != hi_dit; dit++, it++) {
        *it = dit->get()->getPetscGlobalDofIdx();
      }
      // create is with global dofs
      IS is;
      CHKERR ISCreateGeneral(m_field.get_comm(), nb, &*main_indices.begin(),
                             PETSC_USE_POINTER, &is);
      // create map form main problem global indices to out problem global
      // indices
      AO ao;
      CHKERR AOCreateMappingIS(is, PETSC_NULLPTR, &ao);
      if (ss == 0) {
        IS is_dup;
        CHKERR ISDuplicate(is, &is_dup);
        out_problem_it->getSubData()->rowIs = SmartPetscObj<IS>(is_dup, false);
        out_problem_it->getSubData()->rowMap = SmartPetscObj<AO>(ao, true);
      } else {
        IS is_dup;
        CHKERR ISDuplicate(is, &is_dup);
        out_problem_it->getSubData()->colIs = SmartPetscObj<IS>(is_dup, false);
        out_problem_it->getSubData()->colMap = SmartPetscObj<AO>(ao, true);
      }
      CHKERR AOApplicationToPetscIS(ao, is);
      // set global number of DOFs
      CHKERR ISGetSize(is, nb_dofs[ss]);
      CHKERR ISDestroy(&is);
      // set out problem global indices after applying map
      dit = out_problem_dofs[ss]->get<PetscLocalIdx_mi_tag>().lower_bound(0);
      for (std::vector<int>::iterator it = main_indices.begin(); dit != hi_dit;
           dit++, it++) {
        bool success = out_problem_dofs[ss]->modify(
            out_problem_dofs[ss]->project<0>(dit),
            NumeredDofEntity_part_and_all_indices_change(
                dit->get()->getPart(), *it, *it,
                dit->get()->getPetscLocalDofIdx()));
        if (!success) {
          SETERRQ(PETSC_COMM_WORLD, MOFEM_ATOM_TEST_INVALID,
                  "operation unsuccessful");
        }
      }
      // set global indices to nodes not on this part
      {
        NumeredDofEntityByLocalIdx::iterator dit =
            out_problem_dofs[ss]->get<PetscLocalIdx_mi_tag>().lower_bound(-1);
        NumeredDofEntityByLocalIdx::iterator hi_dit =
            out_problem_dofs[ss]->get<PetscLocalIdx_mi_tag>().upper_bound(-1);
        const int nb = std::distance(dit, hi_dit);
        std::vector<int> main_indices_non_local(nb);
        for (auto it = main_indices_non_local.begin(); dit != hi_dit;
             dit++, it++) {
          *it = dit->get()->getPetscGlobalDofIdx();
        }
        IS is;
        CHKERR ISCreateGeneral(m_field.get_comm(), nb,
                               &*main_indices_non_local.begin(),
                               PETSC_USE_POINTER, &is);
        CHKERR AOApplicationToPetscIS(ao, is);
        CHKERR ISDestroy(&is);
        dit = out_problem_dofs[ss]->get<PetscLocalIdx_mi_tag>().lower_bound(-1);
        for (auto it = main_indices_non_local.begin(); dit != hi_dit;
             dit++, it++) {
          bool success = out_problem_dofs[ss]->modify(
              out_problem_dofs[ss]->project<0>(dit),
              NumeredDofEntity_part_and_all_indices_change(
                  dit->get()->getPart(), dit->get()->getDofIdx(), *it,
                  dit->get()->getPetscLocalDofIdx()));
          if (!success) {
            SETERRQ(PETSC_COMM_WORLD, MOFEM_ATOM_TEST_INVALID,
                    "operation unsuccessful");
          }
        }
      }
      CHKERR AODestroy(&ao);
    }
  }
 
  if (square_matrix) {
    out_problem_it->numeredColDofsPtr = out_problem_it->numeredRowDofsPtr;
    out_problem_it->nbLocDofsCol = out_problem_it->nbLocDofsRow;
    out_problem_it->nbDofsCol = out_problem_it->nbDofsRow;
    out_problem_it->getSubData()->colIs = out_problem_it->getSubData()->rowIs;
    out_problem_it->getSubData()->colMap = out_problem_it->getSubData()->rowMap;
  }
 
  CHKERR printPartitionedProblem(&*out_problem_it, verb);
  CHKERR debugPartitionedProblem(&*out_problem_it, verb);
 
  MoFEMFunctionReturn(0);
}

debugPartitionedProblem()

MoFEMErrorCode MoFEM::ProblemsManager::debugPartitionedProblem	(	const Problem *	problem_ptr,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

Debug partition information.

Performs detailed analysis and validation of problem partitioning, checking for inconsistencies and reporting partition quality metrics.

Parameters

problem_ptr	pointer to the problem structure
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 2080 of file ProblemsManager.cpp.

                                                                             {
  MoFEM::Interface &m_field = cOre;
  MoFEMFunctionBeginHot;
 
  auto save_ent = [](moab::Interface &moab, const std::string name,
                     const EntityHandle ent) {
    MoFEMFunctionBegin;
    EntityHandle out_meshset;
    CHKERR moab.create_meshset(MESHSET_SET, out_meshset);
    CHKERR moab.add_entities(out_meshset, &ent, 1);
    CHKERR moab.write_file(name.c_str(), "VTK", "", &out_meshset, 1);
    CHKERR moab.delete_entities(&out_meshset, 1);
    MoFEMFunctionReturn(0);
  };
 
  if (debug > 0) {
 
    typedef NumeredDofEntity_multiIndex::index<Idx_mi_tag>::type
        NumeredDofEntitysByIdx;
    NumeredDofEntitysByIdx::iterator dit, hi_dit;
    const NumeredDofEntitysByIdx *numered_dofs_ptr[] = {
        &(problem_ptr->numeredRowDofsPtr->get<Idx_mi_tag>()),
        &(problem_ptr->numeredColDofsPtr->get<Idx_mi_tag>())};
 
    int *nbdof_ptr[] = {&problem_ptr->nbDofsRow, &problem_ptr->nbDofsCol};
    int *local_nbdof_ptr[] = {&problem_ptr->nbLocDofsRow,
                              &problem_ptr->nbLocDofsCol};
 
    for (int ss = 0; ss < 2; ss++) {
 
      dit = numered_dofs_ptr[ss]->begin();
      hi_dit = numered_dofs_ptr[ss]->end();
      for (; dit != hi_dit; dit++) {
        if ((*dit)->getPart() == (unsigned int)m_field.get_comm_rank()) {
          if ((*dit)->getPetscLocalDofIdx() < 0) {
            std::ostringstream zz;
            zz << "rank " << m_field.get_comm_rank() << " " << **dit;
            SETERRQ(PETSC_COMM_SELF, MOFEM_IMPOSSIBLE_CASE,
                     "local dof index for %d (0-row, 1-col) not set, i.e. has "
                     "negative value\n %s",
                     ss, zz.str().c_str());
          }
          if ((*dit)->getPetscLocalDofIdx() >= *local_nbdof_ptr[ss]) {
            std::ostringstream zz;
            zz << "rank " << m_field.get_comm_rank() << " " << **dit;
            SETERRQ(PETSC_COMM_SELF, MOFEM_IMPOSSIBLE_CASE,
                     "local dofs for %d (0-row, 1-col) out of range\n %s", ss,
                     zz.str().c_str());
          }
        } else {
          if ((*dit)->getPetscGlobalDofIdx() < 0) {
 
            const EntityHandle ent = (*dit)->getEnt();
            CHKERR save_ent(
                m_field.get_moab(),
                "debug_part" +
                    boost::lexical_cast<std::string>(m_field.get_comm_rank()) +
                    "_negative_global_index.vtk",
                ent);
 
            std::ostringstream zz;
            zz << "rank " << m_field.get_comm_rank() << " "
               << dit->get()->getBitRefLevel() << " " << **dit;
            SETERRQ(PETSC_COMM_SELF, MOFEM_IMPOSSIBLE_CASE,
                     "global dof index for %d (0-row, 1-col) row not set, i.e. "
                     "has negative value\n %s",
                     ss, zz.str().c_str());
          }
          if ((*dit)->getPetscGlobalDofIdx() >= *nbdof_ptr[ss]) {
            std::ostringstream zz;
            zz << "rank " << m_field.get_comm_rank() << " nb_dofs "
               << *nbdof_ptr[ss] << " " << **dit;
            SETERRQ(PETSC_COMM_SELF, MOFEM_IMPOSSIBLE_CASE,
                     "global dofs for %d (0-row, 1-col) out of range\n %s", ss,
                     zz.str().c_str());
          }
        }
      }
    }
  }
  MoFEMFunctionReturnHot(0);
}

getFEMeshset()

MoFEMErrorCode MoFEM::ProblemsManager::getFEMeshset	(	const std::string	prb_name,
		const std::string &	fe_name,
		EntityHandle *	meshset
	)		const

#include <src/interfaces/ProblemsManager.hpp>

Create finite element meshset for the problem.

Creates or retrieves the meshset entity that contains all finite elements of a specific type within a problem. The meshset entity must be created before calling this function.

Parameters

prb_name	name of the problem
fe_name	name of the finite element type
meshset	pointer to store the meshset handle

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 2564 of file ProblemsManager.cpp.

                                                                          {
  MoFEM::Interface &m_field = cOre;
  const Problem *problem_ptr;
  const FiniteElement_multiIndex *fes_ptr;
  ProblemManagerFunctionBegin;
 
  CHKERR m_field.get_moab().create_meshset(MESHSET_SET, *meshset);
  CHKERR m_field.get_problem(prb_name, &problem_ptr);
  CHKERR m_field.get_finite_elements(&fes_ptr);
 
  auto fe_miit = fes_ptr->get<FiniteElement_name_mi_tag>().find(fe_name);
  if (fe_miit != fes_ptr->get<FiniteElement_name_mi_tag>().end()) {
    auto fit =
        problem_ptr->numeredFiniteElementsPtr->get<Unique_mi_tag>().lower_bound(
            EntFiniteElement::getLocalUniqueIdCalculate(
                0, (*fe_miit)->getFEUId()));
    auto hi_fe_it =
        problem_ptr->numeredFiniteElementsPtr->get<Unique_mi_tag>().upper_bound(
            EntFiniteElement::getLocalUniqueIdCalculate(
                get_id_for_max_type<MBENTITYSET>(), (*fe_miit)->getFEUId()));
    std::vector<EntityHandle> fe_vec;
    fe_vec.reserve(std::distance(fit, hi_fe_it));
    for (; fit != hi_fe_it; fit++)
      fe_vec.push_back(fit->get()->getEnt());
    CHKERR m_field.get_moab().add_entities(*meshset, &*fe_vec.begin(),
                                           fe_vec.size());
  }
 
  MoFEMFunctionReturn(0);
}

getOptions()

MoFEMErrorCode MoFEM::ProblemsManager::getOptions

(

)

#include <src/interfaces/ProblemsManager.hpp>

Get command line options for ProblemsManager.

Retrieves configuration options from command line arguments that control problem building behavior, such as buildProblemFromFields and synchroniseProblemEntities flags.

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 62 of file ProblemsManager.cpp.

                                           {
  MoFEM::Interface &m_field = cOre;
  MoFEMFunctionBeginHot;
  PetscOptionsBegin(m_field.get_comm(), "", "Problem manager", "none");
  {
    CHKERR PetscOptionsBool(
        "-problem_build_from_fields",
        "Add DOFs to problem directly from fields not through DOFs on elements",
        "", buildProblemFromFields, &buildProblemFromFields, NULL);
  }
  PetscOptionsEnd();
  MoFEMFunctionReturnHot(0);
}

getProblemElementsLayout()

MoFEMErrorCode MoFEM::ProblemsManager::getProblemElementsLayout	(	const std::string	name,
		const std::string &	fe_name,
		PetscLayout *	layout
	)		const

#include <src/interfaces/ProblemsManager.hpp>

Get layout of elements in the problem.

In layout is stored information how many elements is on each processor, for more information look int petsc documentation http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/IS/PetscLayoutCreate.html#PetscLayoutCreate

Parameters

name	problem name
fe_name	finite elements
layout	layout
verb	verbosity level

Returns

error code

Definition at line 2598 of file ProblemsManager.cpp.

                                                                     {
  MoFEM::Interface &m_field = cOre;
  const Problem *problem_ptr;
  ProblemManagerFunctionBegin;
  CHKERR m_field.get_problem(name, &problem_ptr);
  CHKERR problem_ptr->getNumberOfElementsByNameAndPart(PETSC_COMM_WORLD,
                                                       fe_name, layout);
  MoFEMFunctionReturn(0);
}

getSideDofsOnBrokenSpaceEntities()

MoFEMErrorCode MoFEM::ProblemsManager::getSideDofsOnBrokenSpaceEntities	(	std::vector< boost::weak_ptr< NumeredDofEntity > > &	vec_dof_view,
		const std::string	problem_name,
		RowColData	rc,
		const std::string	field_name,
		const Range	ents,
		int	bridge_dim,
		const int	lo_coeff = 0,
		const int	hi_coeff = MAX_DOFS_ON_ENTITY,
		const int	lo_order = 0,
		const int	hi_order = 100,
		int	verb = VERBOSE,
		const bool	debug = false
	)		const

#include <src/interfaces/ProblemsManager.hpp>

Get DOFs on side entities for broken space.

Retrieves DOFs associated with side entities in broken (discontinuous) spaces. The DOFs are connected through a bridge entity of specified dimension. This is useful for implementing interface conditions in discontinuous Galerkin methods.

Parameters

vec_dof_view	output vector to store the DOF entities
problem_name	name of the problem
rc	row or column data specification
field_name	name of the field
ents	range of side entities to process
bridge_dim	dimension of bridge entity connecting DOFs to side entities
lo_coeff	lowest coefficient (rank) to include
hi_coeff	highest coefficient (rank) to include
lo_order	lowest polynomial order to include
hi_order	highest polynomial order to include
verb	verbosity level
debug	enable debug output for inconsistency checking

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 2610 of file ProblemsManager.cpp.

        {
  MoFEM::Interface &m_field = cOre;
  ProblemManagerFunctionBegin;
 
  switch (rc) {
  case ROW:
  case COL:
    break;
  default:
    SETERRQ(m_field.get_comm(), MOFEM_INVALID_DATA, "invalid RowColData");
    break;
  }
 
  const Problem *prb_ptr;
  CHKERR m_field.get_problem(problem_name, &prb_ptr);
 
  decltype(prb_ptr->numeredRowDofsPtr) numered_dofs[2] = {
      prb_ptr->numeredRowDofsPtr, nullptr};
  if (prb_ptr->numeredRowDofsPtr != prb_ptr->numeredColDofsPtr)
    numered_dofs[1] = prb_ptr->numeredColDofsPtr;
 
  Range bridge_ents;
  CHKERR m_field.get_moab().get_adjacencies(
      ents, bridge_dim, false, bridge_ents, moab::Interface::UNION);
 
  auto &moab = m_field.get_moab();
  const auto bit_number = m_field.get_field_bit_number(field_name);
  const auto nb_coeffs =
      m_field.get_field_structure(field_name)->getNbOfCoeffs();
  const auto &side_dof_map = m_field.get_field_structure(field_name)
                                 ->getDofSideMap();
 
  using NumeredDofEntity_it_view_multiIndex = multi_index_container<
 
      NumeredDofEntity_multiIndex::iterator, indexed_by<sequenced<>>
 
      >;
  NumeredDofEntity_it_view_multiIndex dofs_it_view;
 
  for (auto pit = bridge_ents.const_pair_begin();
       pit != bridge_ents.const_pair_end(); ++pit) {
    auto lo = numered_dofs[rc]->get<Unique_mi_tag>().lower_bound(
        DofEntity::getLoFieldEntityUId(bit_number, pit->first));
    auto hi = numered_dofs[rc]->get<Unique_mi_tag>().upper_bound(
        DofEntity::getHiFieldEntityUId(bit_number, pit->second));
 
    auto bride_type = moab.type_from_handle(pit->first);
 
    for (; lo != hi; ++lo) {
      if ((*lo)->getDofCoeffIdx() >= lo_coeff &&
          (*lo)->getDofCoeffIdx() <= hi_coeff &&
          (*lo)->getDofOrder() >= lo_order &&
          (*lo)->getDofOrder() <= hi_order) {
        auto ent_dof_index = (*lo)->getEntDofIdx();
        auto side_it = side_dof_map.at(bride_type)
                           .get<EntDofIdx_mi_tag>()
                           .find(std::floor(static_cast<double>(ent_dof_index) /
                                            nb_coeffs));
        if (side_it !=
            side_dof_map.at(bride_type).get<EntDofIdx_mi_tag>().end()) {
          auto bridge_ent = (*lo)->getEnt();
          auto type = side_it->type;
          auto side = side_it->side;
          auto dim = CN::Dimension(type);
          EntityHandle side_ent = 0;
          CHKERR moab.side_element(bridge_ent, dim, side, side_ent);
          if (ents.find(side_ent) != ents.end()) {
            dofs_it_view.emplace_back(numered_dofs[rc]->project<0>(lo));
          }
        } else {
#ifndef NDEBUG
          MOFEM_LOG("SELF", Sev::error)
              << *m_field.get_field_structure(field_name);
          MOFEM_LOG("SELF", Sev::error)
              << "side not found for entity " << CN::EntityTypeName(bride_type);
          MOFEM_LOG("SELF", Sev::error)
              << "ent_dof_index / nb_coeffs "
              << std::floor(static_cast<double>(ent_dof_index) / nb_coeffs);
          MOFEM_LOG("SELF", Sev::error)
              << "side_dof_map.size() " << side_dof_map.size();
#endif // NDEBUG
          SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                  "side not found - you will get more information in debug");
        }
      }
    }
  }
 
  if (verb > QUIET) {
    for (auto &dof : dofs_it_view)
      MOFEM_LOG("SYNC", Sev::noisy) << **dof;
    MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::noisy);
  }
 
  vec_dof_view.reserve(vec_dof_view.size() + dofs_it_view.size());
  for (auto dit : dofs_it_view)
    vec_dof_view.push_back(*dit);
 
  MoFEMFunctionReturn(0);
}

inheritPartition()

MoFEMErrorCode MoFEM::ProblemsManager::inheritPartition	(	const std::string	name,
		const std::string	problem_for_rows,
		bool	copy_rows,
		const std::string	problem_for_cols,
		bool	copy_cols,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

build indexing and partition problem inheriting indexing and partitioning from two other problems

Transfers DOF indexing and partitioning information from existing problems to a new problem. This is useful for maintaining consistent partitioning across related problems in multi-physics simulations.

Parameters

name	name of the target problem to inherit partitioning
problem_for_rows	source problem for row DOF indexing and partitioning
copy_rows	if true, copy row DOF indices; if false, only copy partition info
problem_for_cols	source problem for column DOF indexing and partitioning
copy_cols	if true, copy column DOF indices; if false, only copy partition info
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

If copy_rows/copy_cols is set to false only partition is copied between problems.

Examples

mofem/atom_tests/build_problems.cpp.

Definition at line 1892 of file ProblemsManager.cpp.

                                                                {
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  ProblemManagerFunctionBegin;
 
  if (!(cOre.getBuildMoFEM() & Core::BUILD_PROBLEM))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY, "pRoblems not build");
 
  typedef Problem_multiIndex::index<Problem_mi_tag>::type ProblemByName;
 
  // find p_miit
  ProblemByName &problems_by_name =
      const_cast<ProblemByName &>(problems_ptr->get<Problem_mi_tag>());
  ProblemByName::iterator p_miit = problems_by_name.find(name);
  if (p_miit == problems_by_name.end()) {
    SETERRQ(m_field.get_comm(), MOFEM_NOT_FOUND,
             "problem with name < %s > not defined (top tip check spelling)",
             name.c_str());
  }
  if (verb > QUIET)
    MOFEM_LOG("WORLD", Sev::inform)
        << p_miit->getName() << " from rows of " << problem_for_rows
        << " and columns of " << problem_for_cols;
 
  // find p_miit_row
  ProblemByName::iterator p_miit_row = problems_by_name.find(problem_for_rows);
  if (p_miit_row == problems_by_name.end()) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
             "problem with name < %s > not defined (top tip check spelling)",
             problem_for_rows.c_str());
  }
  const boost::shared_ptr<NumeredDofEntity_multiIndex> dofs_row =
      p_miit_row->numeredRowDofsPtr;
 
  // find p_mit_col
  ProblemByName::iterator p_miit_col = problems_by_name.find(problem_for_cols);
  if (p_miit_col == problems_by_name.end()) {
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
             "problem with name < %s > not defined (top tip check spelling)",
             problem_for_cols.c_str());
  }
  boost::shared_ptr<NumeredDofEntity_multiIndex> dofs_col =
      p_miit_col->numeredColDofsPtr;
 
  bool copy[] = {copy_rows, copy_cols};
  boost::shared_ptr<NumeredDofEntity_multiIndex> composed_dofs[] = {
      p_miit->numeredRowDofsPtr, p_miit->numeredColDofsPtr};
 
  int *nb_local_dofs[] = {&p_miit->nbLocDofsRow, &p_miit->nbLocDofsCol};
  int *nb_dofs[] = {&p_miit->nbDofsRow, &p_miit->nbDofsCol};
  boost::shared_ptr<NumeredDofEntity_multiIndex> copied_dofs[] = {dofs_row,
                                                                  dofs_col};
 
  for (int ss = 0; ss < 2; ss++) {
 
    // build indices
    *nb_local_dofs[ss] = 0;
    if (!copy[ss]) {
 
      // only copy indices which are belong to some elements if this problem
      std::vector<int> is_local, is_new;
 
      NumeredDofEntityByUId &dofs_by_uid =
          copied_dofs[ss]->get<Unique_mi_tag>();
      for (NumeredDofEntity_multiIndex::iterator dit =
               composed_dofs[ss]->begin();
           dit != composed_dofs[ss]->end(); dit++) {
        NumeredDofEntityByUId::iterator diit =
            dofs_by_uid.find((*dit)->getLocalUniqueId());
        if (diit == dofs_by_uid.end()) {
          SETERRQ(
              m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
              "data inconsistency, could not find dof in composite problem");
        }
        int part_number = (*diit)->getPart(); // get part number
        int petsc_global_dof = (*diit)->getPetscGlobalDofIdx();
        bool success;
        success = composed_dofs[ss]->modify(
            dit, NumeredDofEntity_part_and_glob_idx_change(part_number,
                                                           petsc_global_dof));
        if (!success) {
          SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        }
        if ((*dit)->getPart() == (unsigned int)m_field.get_comm_rank()) {
          success = composed_dofs[ss]->modify(
              dit, NumeredDofEntity_local_idx_change((*nb_local_dofs[ss])++));
          if (!success) {
            SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
          }
          is_local.push_back(petsc_global_dof);
        }
      }
 
      AO ao;
      CHKERR AOCreateMapping(m_field.get_comm(), is_local.size(), &is_local[0],
                             NULL, &ao);
 
      // apply local to global mapping
      is_local.resize(0);
      for (NumeredDofEntity_multiIndex::iterator dit =
               composed_dofs[ss]->begin();
           dit != composed_dofs[ss]->end(); dit++) {
        is_local.push_back((*dit)->getPetscGlobalDofIdx());
      }
      CHKERR AOPetscToApplication(ao, is_local.size(), &is_local[0]);
      int idx2 = 0;
      for (NumeredDofEntity_multiIndex::iterator dit =
               composed_dofs[ss]->begin();
           dit != composed_dofs[ss]->end(); dit++) {
        int part_number = (*dit)->getPart(); // get part number
        int petsc_global_dof = is_local[idx2++];
        bool success;
        success = composed_dofs[ss]->modify(
            dit, NumeredDofEntity_part_and_glob_idx_change(part_number,
                                                           petsc_global_dof));
        if (!success) {
          SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        }
      }
 
      CHKERR AODestroy(&ao);
 
    } else {
 
      for (NumeredDofEntity_multiIndex::iterator dit = copied_dofs[ss]->begin();
           dit != copied_dofs[ss]->end(); dit++) {
        std::pair<NumeredDofEntity_multiIndex::iterator, bool> p;
        p = composed_dofs[ss]->insert(boost::shared_ptr<NumeredDofEntity>(
            new NumeredDofEntity((*dit)->getDofEntityPtr())));
        if (p.second) {
          (*nb_dofs[ss])++;
        }
        int dof_idx = (*dit)->getDofIdx();
        int part_number = (*dit)->getPart(); // get part number
        int petsc_global_dof = (*dit)->getPetscGlobalDofIdx();
        if (part_number == (unsigned int)m_field.get_comm_rank()) {
          const bool success = composed_dofs[ss]->modify(
              p.first, NumeredDofEntity_part_and_all_indices_change(
                           part_number, dof_idx, petsc_global_dof,
                           (*nb_local_dofs[ss])++));
          if (!success) {
            SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
          }
        } else {
          const bool success = composed_dofs[ss]->modify(
              p.first, NumeredDofEntity_part_and_mofem_glob_idx_change(
                           part_number, dof_idx, petsc_global_dof));
          if (!success) {
            SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
          }
        }
      }
    }
  }
 
  CHKERR printPartitionedProblem(&*p_miit, verb);
  CHKERR debugPartitionedProblem(&*p_miit, verb);
 
  MoFEMFunctionReturn(0);
}

markDofs()

MoFEMErrorCode MoFEM::ProblemsManager::markDofs	(	const std::string	problem_name,
		RowColData	rc,
		std::vector< boost::weak_ptr< NumeredDofEntity > > &	vec_dof_view,
		const enum MarkOP	op,
		std::vector< unsigned char > &	marker
	)		const

#include <src/interfaces/ProblemsManager.hpp>

Create vector with marked DOF indices based on DOF view.

Creates or modifies a marker vector based on a DOF view, allowing selective marking of DOFs that are present in the view. This is useful for creating masks or index sets for specific DOF collections in matrix/vector operations.

Parameters

problem_name	name of the problem
rc	row or column data specification
vec_dof_view	vector of DOF entities to process for marking
op	marking operation (OR, AND, XOR) to apply
marker	reference to marker vector to create/modify

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 3656 of file ProblemsManager.cpp.

        {
  Interface &m_field = cOre;
  ProblemManagerFunctionBegin;
 
  const Problem *problem_ptr;
  CHKERR m_field.get_problem(problem_name, &problem_ptr);
  boost::shared_ptr<NumeredDofEntity_multiIndex> dofs;
  switch (rc) {
  case ROW:
    dofs = problem_ptr->getNumeredRowDofsPtr();
    break;
  case COL:
    dofs = problem_ptr->getNumeredColDofsPtr();
    break;
  default:
    SETERRQ(PETSC_COMM_SELF, MOFEM_IMPOSSIBLE_CASE, "Should be row or column");
  }
  marker.resize(dofs->size(), 0);
 
  for (auto &dof : vec_dof_view) {
    if (auto dof_ptr = dof.lock()) {
      if (dof_ptr->getPetscLocalDofIdx() < 0)
        continue;
      if (op == MarkOP::OR)
        marker[dof_ptr->getPetscLocalDofIdx()] |= 1;
      else
        marker[dof_ptr->getPetscLocalDofIdx()] &= 1;
    }
  }
 
  MoFEMFunctionReturn(0);
}

modifyMarkDofs()

MoFEMErrorCode MoFEM::ProblemsManager::modifyMarkDofs	(	const std::string	problem_name,
		RowColData	rc,
		const std::string	field_name,
		const int	lo,
		const int	hi,
		const enum MarkOP	op,
		const unsigned char	c,
		std::vector< unsigned char > &	marker
	)		const

#include <src/interfaces/ProblemsManager.hpp>

Modify DOF markers for specific field and coefficient range.

Modifies the marker flags for DOFs associated with a specific field within a defined coefficient range. This allows selective marking/unmarking of DOFs based on field and polynomial order criteria using bitwise operations.

Parameters

problem_name	name of the problem
rc	row or column data specification
field_name	name of the field to process
lo	lowest coefficient (rank) to include
hi	highest coefficient (rank) to include
op	marking operation (OR, AND, XOR) to apply
c	marker value to apply with the operation
marker	reference to marker vector to modify

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 3606 of file ProblemsManager.cpp.

                                                                   {
 
  Interface &m_field = cOre;
  const Problem *problem_ptr;
  ProblemManagerFunctionBegin;
  CHKERR m_field.get_problem(problem_name, &problem_ptr);
  boost::shared_ptr<NumeredDofEntity_multiIndex> dofs;
  switch (rc) {
  case ROW:
    dofs = problem_ptr->getNumeredRowDofsPtr();
    break;
  case COL:
    dofs = problem_ptr->getNumeredColDofsPtr();
  default:
    SETERRQ(PETSC_COMM_SELF, MOFEM_IMPOSSIBLE_CASE, "Should be row or column");
  }
  marker.resize(dofs->size(), 0);
 
  auto dof_lo = dofs->get<Unique_mi_tag>().lower_bound(
      FieldEntity::getLoBitNumberUId(m_field.get_field_bit_number(field_name)));
  auto dof_hi = dofs->get<Unique_mi_tag>().upper_bound(
      FieldEntity::getHiBitNumberUId(m_field.get_field_bit_number(field_name)));
 
  switch (op) {
  case MarkOP::OR:
    for (; dof_lo != dof_hi; ++dof_lo) {
      if ((*dof_lo)->getPetscLocalDofIdx() < 0)
        continue;
      if ((*dof_lo)->getDofCoeffIdx() >= lo &&
          (*dof_lo)->getDofCoeffIdx() <= hi)
        marker[(*dof_lo)->getPetscLocalDofIdx()] |= c;
    }
    break;
  case MarkOP::AND:
    for (; dof_lo != dof_hi; ++dof_lo) {
      if ((*dof_lo)->getPetscLocalDofIdx() < 0)
        continue;
      if ((*dof_lo)->getDofCoeffIdx() >= lo &&
          (*dof_lo)->getDofCoeffIdx() <= hi)
        marker[(*dof_lo)->getPetscLocalDofIdx()] &= c;
    }
    break;
  }
 
  MoFEMFunctionReturn(0);
}

partitionFiniteElements()

MoFEMErrorCode MoFEM::ProblemsManager::partitionFiniteElements	(	const std::string	name,
		bool	part_from_moab = false,
		int	low_proc = -1,
		int	hi_proc = -1,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

partition finite elements

Function which partition finite elements based on dofs partitioning. In addition it sets information about local row and cols dofs at given element on partition. Can optionally use MOAB's partitioning information or restrict partitioning to specific processor ranges.

Parameters

name	problem name to partition finite elements for
part_from_moab	if true, use MOAB's existing partition information
low_proc	lowest processor rank to include (-1 for all)
hi_proc	highest processor rank to include (-1 for all)
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Examples

mofem/atom_tests/build_composite_problem.cpp, mofem/atom_tests/build_problems.cpp, mofem/atom_tests/continuity_check_on_skeleton_3d.cpp, mofem/atom_tests/forces_and_sources_testing_edge_element.cpp, mofem/atom_tests/forces_and_sources_testing_flat_prism_element.cpp, mofem/atom_tests/hcurl_divergence_operator_2d.cpp, mofem/atom_tests/mesh_insert_interface_atom.cpp, mofem/atom_tests/prism_elements_from_surface.cpp, mofem/atom_tests/prism_polynomial_approximation.cpp, mofem/atom_tests/quad_polynomial_approximation.cpp, mofem/atom_tests/remove_entities_from_problem.cpp, and mofem/users_modules/basic_finite_elements/nonlinear_elasticity/nonlinear_dynamics.cpp.

Definition at line 2163 of file ProblemsManager.cpp.

                                                                               {
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  auto fe_ent_ptr = m_field.get_ents_finite_elements();
  ProblemManagerFunctionBegin;
 
  if (!(cOre.getBuildMoFEM() & Core::BUILD_FIELD))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY, "fields not build");
 
  if (!(cOre.getBuildMoFEM() & Core::BUILD_FE))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY, "FEs not build");
 
  if (!(cOre.getBuildMoFEM() & Core::BUILD_ADJ))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "adjacencies not build");
 
  if (!(cOre.getBuildMoFEM() & Core::BUILD_PROBLEM))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY, "problem not build");
 
  if (!(cOre.getBuildMoFEM() & Core::PARTITION_PROBLEM))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "problem not partitioned");
 
  if (low_proc == -1)
    low_proc = m_field.get_comm_rank();
  if (hi_proc == -1)
    hi_proc = m_field.get_comm_rank();
 
  // Find pointer to problem of given name
  typedef Problem_multiIndex::index<Problem_mi_tag>::type ProblemByName;
  auto &problems =
      const_cast<ProblemByName &>(problems_ptr->get<Problem_mi_tag>());
  ProblemByName::iterator p_miit = problems.find(name);
  if (p_miit == problems.end()) {
    SETERRQ(m_field.get_comm(), MOFEM_NOT_FOUND,
             "problem < %s > not found (top tip: check spelling)",
             name.c_str());
  }
 
  // Get reference on finite elements multi-index on the problem
  NumeredEntFiniteElement_multiIndex &problem_finite_elements =
      *p_miit->numeredFiniteElementsPtr;
 
  // Clear all elements and data, build it again
  problem_finite_elements.clear();
 
  // Check if dofs and columns are the same, i.e. structurally symmetric
  // problem
  bool do_cols_prob = true;
  if (p_miit->numeredRowDofsPtr == p_miit->numeredColDofsPtr) {
    do_cols_prob = false;
  }
 
  auto get_good_elems = [&]() {
    auto good_elems = std::vector<decltype(fe_ent_ptr->begin())>();
    good_elems.reserve(fe_ent_ptr->size());
 
    const auto prb_bit = p_miit->getBitRefLevel();
    const auto prb_mask = p_miit->getBitRefLevelMask();
 
    // Loop over all elements in database and if right element is there add it
    // to problem finite element multi-index
    for (auto efit = fe_ent_ptr->begin(); efit != fe_ent_ptr->end(); ++efit) {
 
      // if element is not part of problem
      if (((*efit)->getId() & p_miit->getBitFEId()).any()) {
 
        const auto &fe_bit = (*efit)->getBitRefLevel();
 
        // if entity is not problem refinement level
        if ((fe_bit & prb_mask) == fe_bit && (fe_bit & prb_bit).any())
          good_elems.emplace_back(efit);
      }
    }
 
    return good_elems;
  };
 
  auto good_elems = get_good_elems();
 
  auto numbered_good_elems_ptr =
      boost::make_shared<std::vector<NumeredEntFiniteElement>>();
  numbered_good_elems_ptr->reserve(good_elems.size());
  for (auto &efit : good_elems)
    numbered_good_elems_ptr->emplace_back(NumeredEntFiniteElement(*efit));
 
  if (!do_cols_prob) {
    for (auto &fe : *numbered_good_elems_ptr) {
      if (fe.sPtr->getRowFieldEntsPtr() == fe.sPtr->getColFieldEntsPtr()) {
        fe.getColFieldEntsPtr() = fe.getRowFieldEntsPtr();
      }
    }
  }
 
  if (part_from_moab) {
    for (auto &fe : *numbered_good_elems_ptr) {
      if (fe.getEntType() == MBENTITYSET) {
        fe.part = m_field.get_comm_rank();
      } else {
        // if partition is taken from moab partition
        int proc = fe.getPartProc();
        if (proc == -1 && fe.getEntType() == MBVERTEX)
          proc = fe.getOwnerProc();
        fe.part = proc;
      }
    }
  }
 
  for (auto &fe : *numbered_good_elems_ptr) {
 
    NumeredDofEntity_multiIndex_uid_view_ordered rows_view;
    CHKERR fe.sPtr->getRowDofView(*(p_miit->numeredRowDofsPtr), rows_view);
 
    if (!part_from_moab) {
      if (fe.getEntType() == MBENTITYSET) {
        fe.part = m_field.get_comm_rank();
      } else {
        std::vector<int> parts(m_field.get_comm_size(), 0);
        for (auto &dof_ptr : rows_view)
          parts[dof_ptr->pArt]++;
        std::vector<int>::iterator pos =
            max_element(parts.begin(), parts.end());
        const auto max_part = std::distance(parts.begin(), pos);
        fe.part = max_part;
      }
    }
  }
 
  for (auto &fe : *numbered_good_elems_ptr) {
 
    auto check_fields_and_dofs = [&]() {
      if (!part_from_moab) {
        if (fe.getBitFieldIdRow().none() && m_field.get_comm_size() == 0) {
          MOFEM_LOG("WORLD", Sev::warning)
              << "At least one field has to be added to element row to "
                 "determine partition of finite element. Check element " +
                     boost::lexical_cast<std::string>(fe.getName());
        }
      }
 
      return true;
    };
 
    if (check_fields_and_dofs()) {
      // Add element to the problem
      auto p = problem_finite_elements.insert(
          boost::shared_ptr<NumeredEntFiniteElement>(numbered_good_elems_ptr,
                                                     &fe));
      if (!p.second)
        SETERRQ(PETSC_COMM_SELF, MOFEM_NOT_FOUND, "element is there");
    }
  }
 
  if (verb >= VERBOSE) {
    auto elements_on_rank =
        problem_finite_elements.get<Part_mi_tag>().equal_range(
            m_field.get_comm_rank());
    MOFEM_LOG("SYNC", Sev::verbose)
        << p_miit->getName() << " nb. elems "
        << std::distance(elements_on_rank.first, elements_on_rank.second);
    auto fe_ptr = m_field.get_finite_elements();
    for (auto &fe : *fe_ptr) {
      auto e_range =
          problem_finite_elements.get<Composite_Name_And_Part_mi_tag>()
              .equal_range(
                  boost::make_tuple(fe->getName(), m_field.get_comm_rank()));
      MOFEM_LOG("SYNC", Sev::noisy)
          << "Element " << fe->getName() << " nb. elems "
          << std::distance(e_range.first, e_range.second);
    }
 
    MOFEM_LOG_SYNCHRONISE(m_field.get_comm());
  }
 
  cOre.getBuildMoFEM() |= Core::PARTITION_FE;
  MoFEMFunctionReturn(0);
}

partitionGhostDofs()

MoFEMErrorCode MoFEM::ProblemsManager::partitionGhostDofs	(	const std::string	name,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

determine ghost nodes

Identifies and marks DOFs as ghost DOFs for parallel computations. DOFs are ghost dofs if they are used by elements on a given partition but not owned by that partition.

Parameters

name	problem name to determine ghost DOFs for
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Examples

mofem/atom_tests/build_composite_problem.cpp, mofem/atom_tests/build_problems.cpp, mofem/atom_tests/continuity_check_on_skeleton_3d.cpp, mofem/atom_tests/forces_and_sources_testing_edge_element.cpp, mofem/atom_tests/forces_and_sources_testing_flat_prism_element.cpp, mofem/atom_tests/hcurl_divergence_operator_2d.cpp, mofem/atom_tests/mesh_insert_interface_atom.cpp, mofem/atom_tests/prism_elements_from_surface.cpp, mofem/atom_tests/prism_polynomial_approximation.cpp, mofem/atom_tests/quad_polynomial_approximation.cpp, mofem/atom_tests/remove_entities_from_problem.cpp, and mofem/users_modules/basic_finite_elements/nonlinear_elasticity/nonlinear_dynamics.cpp.

Definition at line 2344 of file ProblemsManager.cpp.

                                                             {
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  ProblemManagerFunctionBegin;
 
  if (!(cOre.getBuildMoFEM() & Core::PARTITION_PROBLEM))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "partition of problem not build");
  if (!(cOre.getBuildMoFEM() & Core::PARTITION_FE))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "partitions finite elements not build");
 
  // get problem pointer
  auto p_miit = problems_ptr->get<Problem_mi_tag>().find(name);
  if (p_miit == problems_ptr->get<Problem_mi_tag>().end())
    SETERRQ(PETSC_COMM_SELF, MOFEM_INVALID_DATA, "Problem %s not fond",
             name.c_str());
 
  // get reference to number of ghost dofs
  int &nb_row_ghost_dofs = p_miit->nbGhostDofsRow;
  int &nb_col_ghost_dofs = p_miit->nbGhostDofsCol;
  nb_row_ghost_dofs = 0;
  nb_col_ghost_dofs = 0;
 
  // do work if more than one processor
  if (m_field.get_comm_size() > 1) {
 
    NumeredDofEntity_multiIndex_uid_view_ordered ghost_idx_row_view,
        ghost_idx_col_view;
 
    // get elements on this partition
    auto fe_range =
        p_miit->numeredFiniteElementsPtr->get<Part_mi_tag>().equal_range(
            m_field.get_comm_rank());
 
    // get dofs on elements which are not part of this partition
 
    struct Inserter {
      using Vec = std::vector<boost::shared_ptr<NumeredDofEntity>>;
      using It = Vec::iterator;
      It operator()(Vec &dofs_view, It &hint,
                    boost::shared_ptr<NumeredDofEntity> &&dof) {
        dofs_view.emplace_back(dof);
        return dofs_view.end();
      }
    };
 
    // rows
    std::vector<boost::shared_ptr<NumeredDofEntity>> fe_vec_view;
    auto hint_r = ghost_idx_row_view.begin();
    for (auto fe_ptr = fe_range.first; fe_ptr != fe_range.second; ++fe_ptr) {
 
      fe_vec_view.clear();
      CHKERR EntFiniteElement::getDofView((*fe_ptr)->getRowFieldEnts(),
                                          *(p_miit->getNumeredRowDofsPtr()),
                                          fe_vec_view, Inserter());
 
      for (auto &dof_ptr : fe_vec_view) {
        if (dof_ptr->getPart() != (unsigned int)m_field.get_comm_rank()) {
          hint_r = ghost_idx_row_view.emplace_hint(hint_r, dof_ptr);
        }
      }
    }
 
    // columns
    if (p_miit->numeredColDofsPtr == p_miit->numeredRowDofsPtr) {
 
      auto hint_c = ghost_idx_col_view.begin();
      for (auto fe_ptr = fe_range.first; fe_ptr != fe_range.second; ++fe_ptr) {
 
        fe_vec_view.clear();
        CHKERR EntFiniteElement::getDofView((*fe_ptr)->getColFieldEnts(),
                                            *(p_miit->getNumeredColDofsPtr()),
                                            fe_vec_view, Inserter());
 
        for (auto &dof_ptr : fe_vec_view) {
          if (dof_ptr->getPart() != (unsigned int)m_field.get_comm_rank()) {
            hint_c = ghost_idx_col_view.emplace_hint(hint_c, dof_ptr);
          }
        }
      }
    }
 
    int *nb_ghost_dofs[2] = {&nb_row_ghost_dofs, &nb_col_ghost_dofs};
    int nb_local_dofs[2] = {p_miit->nbLocDofsRow, p_miit->nbLocDofsCol};
 
    NumeredDofEntity_multiIndex_uid_view_ordered *ghost_idx_view[2] = {
        &ghost_idx_row_view, &ghost_idx_col_view};
    NumeredDofEntityByUId *dof_by_uid_no_const[2] = {
        &p_miit->numeredRowDofsPtr->get<Unique_mi_tag>(),
        &p_miit->numeredColDofsPtr->get<Unique_mi_tag>()};
 
    int loop_size = 2;
    if (p_miit->numeredColDofsPtr == p_miit->numeredRowDofsPtr) {
      loop_size = 1;
    }
 
    // set local ghost dofs indices
    for (int ss = 0; ss != loop_size; ++ss) {
      for (auto &gid : *ghost_idx_view[ss]) {
        NumeredDofEntityByUId::iterator dof =
            dof_by_uid_no_const[ss]->find(gid->getLocalUniqueId());
        if (PetscUnlikely((*dof)->petscLocalDofIdx != (DofIdx)-1))
          SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                  "inconsistent data, ghost dof already set");
        bool success = dof_by_uid_no_const[ss]->modify(
            dof, NumeredDofEntity_local_idx_change(nb_local_dofs[ss]++));
        if (PetscUnlikely(!success))
          SETERRQ(m_field.get_comm(), MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        (*nb_ghost_dofs[ss])++;
      }
    }
    if (loop_size == 1) {
      (*nb_ghost_dofs[1]) = (*nb_ghost_dofs[0]);
    }
  }
 
  if (verb > QUIET) {
    MOFEM_LOG("SYNC", Sev::inform)
        << " FEs ghost dofs on problem " << p_miit->getName()
        << " Nb. ghost dof " << p_miit->getNbGhostDofsRow() << " by "
        << p_miit->getNbGhostDofsCol() << " Nb. local dof "
        << p_miit->getNbLocalDofsCol() << " by " << p_miit->getNbLocalDofsCol();
 
    MOFEM_LOG_SYNCHRONISE(m_field.get_comm())
  }
 
  cOre.getBuildMoFEM() |= Core::PARTITION_GHOST_DOFS;
  MoFEMFunctionReturn(0);
}

partitionGhostDofsOnDistributedMesh()

MoFEMErrorCode MoFEM::ProblemsManager::partitionGhostDofsOnDistributedMesh	(	const std::string	name,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

determine ghost nodes on distributed meshes

Identifies and marks DOFs as ghost DOFs specifically for distributed meshes. This function is similar to partitionGhostDofs but exploits the fact that the mesh is distributed across processors. DOFs are ghosted if they are shared but not owned by the current partition.

Parameters

name	problem name to determine ghost DOFs for
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Examples

mofem/atom_tests/remove_entities_from_problem.cpp.

Definition at line 2478 of file ProblemsManager.cpp.

                                                               {
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  ProblemManagerFunctionBegin;
 
  if (!(cOre.getBuildMoFEM() & Core::PARTITION_PROBLEM))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "partition of problem not build");
  if (!(cOre.getBuildMoFEM() & Core::PARTITION_FE))
    SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
            "partitions finite elements not build");
 
  // get problem pointer
  typedef Problem_multiIndex::index<Problem_mi_tag>::type ProblemsByName;
  // find p_miit
  ProblemsByName &problems_set =
      const_cast<ProblemsByName &>(problems_ptr->get<Problem_mi_tag>());
  ProblemsByName::iterator p_miit = problems_set.find(name);
 
  // get reference to number of ghost dofs
  // get number of local dofs
  DofIdx *nb_ghost_dofs[2] = {&(p_miit->nbGhostDofsRow),
                              &(p_miit->nbGhostDofsCol)};
  DofIdx nb_local_dofs[2] = {p_miit->nbLocDofsRow, p_miit->nbLocDofsCol};
  for (int ss = 0; ss != 2; ++ss) {
    (*nb_ghost_dofs[ss]) = 0;
  }
 
  // do work if more than one processor
  if (m_field.get_comm_size() > 1) {
    // determine if rows on columns are different from dofs on rows
    int loop_size = 2;
    if (p_miit->numeredColDofsPtr == p_miit->numeredRowDofsPtr) {
      loop_size = 1;
    }
 
    typedef decltype(p_miit->numeredRowDofsPtr) NumbDofTypeSharedPtr;
    NumbDofTypeSharedPtr numered_dofs[] = {p_miit->numeredRowDofsPtr,
                                           p_miit->numeredColDofsPtr};
 
    // iterate over dofs on rows and dofs on columns
    for (int ss = 0; ss != loop_size; ++ss) {
 
      // create dofs view by uid
      auto r = numered_dofs[ss]->get<PetscLocalIdx_mi_tag>().equal_range(-1);
 
      std::vector<NumeredDofEntity_multiIndex::iterator> ghost_idx_view;
      ghost_idx_view.reserve(std::distance(r.first, r.second));
      for (; r.first != r.second; ++r.first)
        ghost_idx_view.emplace_back(numered_dofs[ss]->project<0>(r.first));
 
      auto cmp = [](auto a, auto b) {
        return (*a)->getLocalUniqueId() < (*b)->getLocalUniqueId();
      };
      sort(ghost_idx_view.begin(), ghost_idx_view.end(), cmp);
 
      // iterate over dofs which have negative local index
      for (auto gid_it : ghost_idx_view) {
        bool success = numered_dofs[ss]->modify(
            gid_it, NumeredDofEntity_local_idx_change((nb_local_dofs[ss])++));
        if (!success)
          SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        ++(*nb_ghost_dofs[ss]);
      }
    }
    if (loop_size == 1) {
      (*nb_ghost_dofs[1]) = (*nb_ghost_dofs[0]);
    }
  }
 
  if (verb > QUIET) {
    MOFEM_LOG("SYNC", Sev::inform)
        << " FEs ghost dofs on problem " << p_miit->getName()
        << " Nb. ghost dof " << p_miit->getNbGhostDofsRow() << " by "
        << p_miit->getNbGhostDofsCol() << " Nb. local dof "
        << p_miit->getNbLocalDofsCol() << " by " << p_miit->getNbLocalDofsCol();
 
    MOFEM_LOG_SYNCHRONISE(m_field.get_comm())
  }
 
  cOre.getBuildMoFEM() |= Core::PARTITION_GHOST_DOFS;
  MoFEMFunctionReturn(0);
}

partitionMesh() [1/2]

MoFEMErrorCode MoFEM::CommInterface::partitionMesh	(	const Range &	ents,
		const int	dim,
		const int	adj_dim,
		const int	n_parts,
		Tag *	th_vertex_weights = nullptr,
		Tag *	th_edge_weights = nullptr,
		Tag *	th_part_weights = nullptr,
		int	verb = VERBOSE,
		const bool	debug = false
	)

#include <src/interfaces/CommInterface.hpp>

Set partition tag to each finite element in the problem.

This will use one of the mesh partitioning programs available from PETSc See http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatPartitioningType.html

Parameters

ents	Entities to partition
dim	Dimension of entities to partition
adj_dim	Adjacency dimension
n_parts	Number of partitions
verb	Verbosity level

Returns

Error code

Examples

mofem/atom_tests/build_composite_problem.cpp, and mofem/atom_tests/partition_mesh.cpp.

Definition at line 868 of file CommInterface.cpp.

                                                                               {
  MoFEM::Interface &m_field = cOre;
  MoFEMFunctionBegin;
 
  // get layout
  int rstart, rend, nb_elems;
  {
    PetscLayout layout;
    CHKERR PetscLayoutCreate(m_field.get_comm(), &layout);
    CHKERR PetscLayoutSetBlockSize(layout, 1);
    CHKERR PetscLayoutSetSize(layout, ents.size());
    CHKERR PetscLayoutSetUp(layout);
    CHKERR PetscLayoutGetSize(layout, &nb_elems);
    CHKERR PetscLayoutGetRange(layout, &rstart, &rend);
    CHKERR PetscLayoutDestroy(&layout);
    if (verb >= VERBOSE) {
      MOFEM_LOG("SYNC", Sev::inform)
          << "Finite elements in problem: row lower " << rstart << " row upper "
          << rend << " nb. elems " << nb_elems << " ( " << ents.size() << " )";
      MOFEM_LOG_SYNCHRONISE(m_field.get_comm())
    }
  }
 
  std::vector<EntityHandle> weight_ents;
  weight_ents.reserve(rend - rstart + 1);
 
  struct AdjBridge {
    EntityHandle ent;
    std::vector<int> adj;
    AdjBridge(const EntityHandle ent, std::vector<int> &adj)
        : ent(ent), adj(adj) {}
  };
 
  typedef multi_index_container<
      AdjBridge,
      indexed_by<
 
          hashed_unique<member<AdjBridge, EntityHandle, &AdjBridge::ent>>
 
          >>
      AdjBridgeMap;
 
  auto get_it = [&](auto i) {
    auto it = ents.begin();
    for (; i > 0; --i) {
      if (it == ents.end())
        break;
      ++it;
    }
    return it;
  };
 
  Range proc_ents;
  proc_ents.insert(get_it(rstart), get_it(rend));
  if (proc_ents.size() != rend - rstart)
    SETERRQ(PETSC_COMM_WORLD, MOFEM_DATA_INCONSISTENCY,
            "Wrong number of elements in range %ld != %d", proc_ents.size(),
            rend - rstart);
 
  Range all_dim_ents;
  CHKERR m_field.get_moab().get_adjacencies(
      proc_ents, adj_dim, true, all_dim_ents, moab::Interface::UNION);
 
  AdjBridgeMap adj_bridge_map;
  auto hint = adj_bridge_map.begin();
  std::vector<int> adj;
  for (auto ent : all_dim_ents) {
    Range adj_ents;
    CHKERR m_field.get_moab().get_adjacencies(&ent, 1, dim, false, adj_ents);
    adj_ents = intersect(adj_ents, ents);
    adj.clear();
    adj.reserve(adj_ents.size());
    for (auto a : adj_ents)
      adj.emplace_back(ents.index(a));
    hint = adj_bridge_map.emplace_hint(hint, ent, adj);
  }
 
  int *_i;
  int *_j;
  {
    const int nb_loc_elements = rend - rstart;
    std::vector<int> i(nb_loc_elements + 1, 0), j;
    {
      std::vector<int> row_adj;
      Range::iterator fe_it;
      int ii, jj;
      size_t max_row_size;
      for (fe_it = proc_ents.begin(), ii = rstart, jj = 0, max_row_size = 0;
           fe_it != proc_ents.end(); ++fe_it, ++ii) {
 
        if (type_from_handle(*fe_it) == MBENTITYSET) {
          SETERRQ(PETSC_COMM_SELF, MOFEM_NOT_IMPLEMENTED,
                  "not yet implemented, don't know what to do for meshset "
                  "element");
        } else {
 
          Range dim_ents;
          CHKERR m_field.get_moab().get_adjacencies(&*fe_it, 1, adj_dim, false,
                                                    dim_ents);
          dim_ents = intersect(dim_ents, all_dim_ents);
 
          row_adj.clear();
          for (auto e : dim_ents) {
            auto adj_it = adj_bridge_map.find(e);
            if (adj_it != adj_bridge_map.end()) {
 
              for (const auto idx : adj_it->adj)
                row_adj.push_back(idx);
 
            } else
              SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
                      "Entity not found");
          }
 
          std::sort(row_adj.begin(), row_adj.end());
          auto end = std::unique(row_adj.begin(), row_adj.end());
 
          size_t row_size = std::distance(row_adj.begin(), end);
          max_row_size = std::max(max_row_size, row_size);
          if (j.capacity() < (nb_loc_elements - jj) * max_row_size)
            j.reserve(nb_loc_elements * max_row_size);
 
          i[jj] = j.size();
          auto diag = ents.index(*fe_it);
          for (auto it = row_adj.begin(); it != end; ++it)
            if (*it != diag)
              j.push_back(*it);
        }
 
        ++jj;
 
        if (th_vertex_weights != NULL)
          weight_ents.push_back(*fe_it);
      }
 
      i[jj] = j.size();
    }
 
    CHKERR PetscMalloc(i.size() * sizeof(int), &_i);
    CHKERR PetscMalloc(j.size() * sizeof(int), &_j);
    copy(i.begin(), i.end(), _i);
    copy(j.begin(), j.end(), _j);
  }
 
  // get weights
  int *vertex_weights = NULL;
  if (th_vertex_weights != NULL) {
    CHKERR PetscMalloc(weight_ents.size() * sizeof(int), &vertex_weights);
    CHKERR m_field.get_moab().tag_get_data(*th_vertex_weights,
                                           &*weight_ents.begin(),
                                           weight_ents.size(), vertex_weights);
  }
 
  {
    Mat Adj;
    // Adjacency matrix used to partition problems, f.e. METIS
    CHKERR MatCreateMPIAdj(m_field.get_comm(), rend - rstart, nb_elems, _i, _j,
                           PETSC_NULLPTR, &Adj);
    CHKERR MatSetOption(Adj, MAT_STRUCTURALLY_SYMMETRIC, PETSC_TRUE);
 
    if (debug) {
      Mat A;
      CHKERR MatConvert(Adj, MATMPIAIJ, MAT_INITIAL_MATRIX, &A);
      CHKERR MatView(A, PETSC_VIEWER_DRAW_WORLD);
      std::string wait;
      std::cin >> wait;
      CHKERR MatDestroy(&A);
    }
 
    // run pets to do partitioning
    MOFEM_LOG("WORLD", Sev::verbose) << "Start";
 
    MatPartitioning part;
    IS is;
    CHKERR MatPartitioningCreate(m_field.get_comm(), &part);
 
    CHKERR MatPartitioningSetAdjacency(part, Adj);
    CHKERR MatPartitioningSetFromOptions(part);
    CHKERR MatPartitioningSetNParts(part, n_parts);
    if (th_vertex_weights != NULL) {
      CHKERR MatPartitioningSetVertexWeights(part, vertex_weights);
    }
    CHKERR MatPartitioningApply(part, &is);
 
    MOFEM_LOG("WORLD", Sev::verbose) << "End";
 
    // gather
    IS is_gather, is_num, is_gather_num;
    CHKERR ISAllGather(is, &is_gather);
    CHKERR ISPartitioningToNumbering(is, &is_num);
    CHKERR ISAllGather(is_num, &is_gather_num);
 
    const int *part_number, *gids;
    CHKERR ISGetIndices(is_gather, &part_number);
    CHKERR ISGetIndices(is_gather_num, &gids);
 
    // set partition tag and gid tag to entities
    ParallelComm *pcomm = ParallelComm::get_pcomm(
        &m_field.get_moab(), m_field.get_basic_entity_data_ptr()->pcommID);
    Tag part_tag = pcomm->part_tag();
    CHKERR m_field.get_moab().tag_set_data(part_tag, ents, part_number);
    Tag gid_tag = m_field.get_moab().globalId_tag();
 
    std::map<int, Range> parts_ents;
    {
      // get entities on each part
      Range::iterator eit = ents.begin();
      for (int ii = 0; eit != ents.end(); eit++, ii++) {
        parts_ents[part_number[ii]].insert(*eit);
      }
      Range tagged_sets;
      CHKERR m_field.get_moab().get_entities_by_type_and_tag(
          0, MBENTITYSET, &part_tag, NULL, 1, tagged_sets,
          moab::Interface::UNION);
      if (!tagged_sets.empty())
        CHKERR m_field.get_moab().tag_delete_data(part_tag, tagged_sets);
 
      if (n_parts > (int)tagged_sets.size()) {
        // too few partition sets - create missing ones
        int num_new = n_parts - tagged_sets.size();
        for (int i = 0; i < num_new; i++) {
          EntityHandle new_set;
          CHKERR m_field.get_moab().create_meshset(MESHSET_SET, new_set);
          tagged_sets.insert(new_set);
        }
      } else if (n_parts < (int)tagged_sets.size()) {
        // too many partition sets - delete extras
        int num_del = tagged_sets.size() - n_parts;
        for (int i = 0; i < num_del; i++) {
          EntityHandle old_set = tagged_sets.pop_back();
          CHKERR m_field.get_moab().delete_entities(&old_set, 1);
        }
      }
      // write a tag to those sets denoting they're partition sets, with a
      // value of the proc number
      std::vector<int> dum_ids(n_parts);
      for (int i = 0; i < n_parts; i++)
        dum_ids[i] = i;
      CHKERR m_field.get_moab().tag_set_data(part_tag, tagged_sets,
                                             &*dum_ids.begin());
      CHKERR m_field.get_moab().clear_meshset(tagged_sets);
 
      // get lower dimension entities on each part
      for (int pp = 0; pp != n_parts; pp++) {
        Range dim_ents = parts_ents[pp].subset_by_dimension(dim);
        for (int dd = dim - 1; dd >= 0; dd--) {
          Range adj_ents;
          CHKERR m_field.get_moab().get_adjacencies(
              dim_ents, dd, false, adj_ents, moab::Interface::UNION);
          parts_ents[pp].merge(adj_ents);
        }
      }
      for (int pp = 1; pp != n_parts; pp++) {
        for (int ppp = 0; ppp != pp; ppp++) {
          parts_ents[pp] = subtract(parts_ents[pp], parts_ents[ppp]);
        }
      }
 
      for (int pp = 0; pp != n_parts; pp++) {
        CHKERR m_field.get_moab().add_entities(tagged_sets[pp], parts_ents[pp]);
      }
 
      auto set_part = [&]() {
        MoFEMFunctionBegin;
        for (EntityType t = MBEDGE; t != MBENTITYSET; ++t) {
          for (int pp = 0; pp != n_parts; pp++) {
            Range type_ents = parts_ents[pp].subset_by_type(t);
            CHKERR m_field.get_moab().tag_clear_data(part_tag, type_ents, &pp);
          }
        }
        MoFEMFunctionReturn(0);
      };
 
      auto set_gid = [&]() {
        MoFEMFunctionBegin;
        for (int d = 0; d != 4; ++d) {
 
          void *ptr;
          int count;
 
          int gid = 1; // moab indexing from 1
          for (int pp = 0; pp != n_parts; pp++) {
            Range type_ents = parts_ents[pp].subset_by_dimension(d);
 
            auto eit = type_ents.begin();
            for (; eit != type_ents.end();) {
              CHKERR m_field.get_moab().tag_iterate(
                  gid_tag, eit, type_ents.end(), count, ptr);
              auto gid_tag_ptr = static_cast<int *>(ptr);
              for (; count > 0; --count) {
                *gid_tag_ptr = gid;
                ++eit;
                ++gid;
                ++gid_tag_ptr;
              }
            }
          }
        }
 
        MoFEMFunctionReturn(0);
      };
 
      CHKERR set_part();
      CHKERR set_gid();
    }
 
    if (debug) {
      if (m_field.get_comm_rank() == 0) {
        for (int rr = 0; rr != n_parts; rr++) {
          ostringstream ss;
          ss << "out_part_" << rr << ".vtk";
          MOFEM_LOG("SELF", Sev::inform) << "Save debug part mesh " << ss.str();
          EntityHandle meshset;
          CHKERR m_field.get_moab().create_meshset(MESHSET_SET, meshset);
          CHKERR m_field.get_moab().add_entities(meshset, parts_ents[rr]);
          CHKERR m_field.get_moab().write_file(ss.str().c_str(), "VTK", "",
                                               &meshset, 1);
          CHKERR m_field.get_moab().delete_entities(&meshset, 1);
        }
      }
    }
 
    CHKERR ISRestoreIndices(is_gather, &part_number);
    CHKERR ISRestoreIndices(is_gather_num, &gids);
    CHKERR ISDestroy(&is_num);
    CHKERR ISDestroy(&is_gather_num);
    CHKERR ISDestroy(&is_gather);
    CHKERR ISDestroy(&is);
    CHKERR MatPartitioningDestroy(&part);
    CHKERR MatDestroy(&Adj);
  }
 
  MoFEMFunctionReturn(0);
}

partitionMesh() [2/2]

MoFEMErrorCode MoFEM::ProblemsManager::partitionMesh	(	const Range &	ents,
		const int	dim,
		const int	adj_dim,
		const int	n_parts,
		Tag *	th_vertex_weights = nullptr,
		Tag *	th_edge_weights = nullptr,
		Tag *	th_part_weights = nullptr,
		int	verb = VERBOSE,
		const bool	debug = false
	)

#include <src/interfaces/ProblemsManager.hpp>

Set partition tag to each finite element in the problem.

Deprecated:

Use CommInterface

This will use one of the mesh partitioning programs available from PETSc See http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatPartitioningType.html

Parameters

ents	Entities to partition
dim	Dimension of entities to partition
adj_dim	Adjacency dimension
n_parts	Number of partitions
verb	Verbosity level

Returns

Error code

Definition at line 76 of file ProblemsManager.cpp.

                                {
  return static_cast<MoFEM::Interface &>(cOre)
      .getInterface<CommInterface>()
      ->partitionMesh(ents, dim, adj_dim, n_parts, th_vertex_weights,
                      th_edge_weights, th_part_weights, verb, debug);
}

partitionProblem()

MoFEMErrorCode MoFEM::ProblemsManager::partitionProblem	(	const std::string	name,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

partition problem dofs (collective)

Partitions DOFs for distributed problems where the mesh is already distributed across processors. Must be called collectively on all processors in the communicator.

Parameters

name	problem name to partition
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Examples

mofem/atom_tests/build_problems.cpp, mofem/atom_tests/continuity_check_on_skeleton_3d.cpp, mofem/atom_tests/mesh_insert_interface_atom.cpp, mofem/atom_tests/remove_entities_from_problem_not_partitioned.cpp, and mofem/users_modules/basic_finite_elements/nonlinear_elasticity/nonlinear_dynamics.cpp.

Definition at line 1679 of file ProblemsManager.cpp.

                                                           {
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  ProblemManagerFunctionBegin;
 
  MOFEM_LOG("WORLD", Sev::noisy) << "Partition problem " << name;
 
  using NumeredDofEntitysByIdx =
      NumeredDofEntity_multiIndex::index<Idx_mi_tag>::type;
  using ProblemsByName = Problem_multiIndex::index<Problem_mi_tag>::type;
 
  // Find problem pointer by name
  auto &problems_set =
      const_cast<ProblemsByName &>(problems_ptr->get<Problem_mi_tag>());
  auto p_miit = problems_set.find(name);
  if (p_miit == problems_set.end()) {
    SETERRQ(PETSC_COMM_SELF, MOFEM_INVALID_DATA,
             "problem with name %s not defined (top tip check spelling)",
             name.c_str());
  }
  int nb_dofs_row = p_miit->getNbDofsRow();
 
  if (m_field.get_comm_size() != 1) {
 
    if (!(cOre.getBuildMoFEM() & (1 << 0)))
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "fields not build");
    if (!(cOre.getBuildMoFEM() & (1 << 1)))
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "FEs not build");
    if (!(cOre.getBuildMoFEM() & (1 << 2)))
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
              "entFEAdjacencies not build");
    if (!(cOre.getBuildMoFEM() & (1 << 3)))
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Problems not build");
 
    Mat Adj;
    CHKERR m_field.getInterface<MatrixManager>()
        ->createMPIAdjWithArrays<Idx_mi_tag>(name, &Adj, verb);
 
    int m, n;
    CHKERR MatGetSize(Adj, &m, &n);
    if (verb > VERY_VERBOSE)
      MatView(Adj, PETSC_VIEWER_STDOUT_WORLD);
 
    // partitioning
    MatPartitioning part;
    IS is;
    CHKERR MatPartitioningCreate(m_field.get_comm(), &part);
    CHKERR MatPartitioningSetAdjacency(part, Adj);
    CHKERR MatPartitioningSetFromOptions(part);
    CHKERR MatPartitioningSetNParts(part, m_field.get_comm_size());
    CHKERR MatPartitioningApply(part, &is);
    if (verb > VERY_VERBOSE)
      ISView(is, PETSC_VIEWER_STDOUT_WORLD);
 
    // gather
    IS is_gather, is_num, is_gather_num;
    CHKERR ISAllGather(is, &is_gather);
    CHKERR ISPartitioningToNumbering(is, &is_num);
    CHKERR ISAllGather(is_num, &is_gather_num);
    const int *part_number, *petsc_idx;
    CHKERR ISGetIndices(is_gather, &part_number);
    CHKERR ISGetIndices(is_gather_num, &petsc_idx);
    int size_is_num, size_is_gather;
    CHKERR ISGetSize(is_gather, &size_is_gather);
    if (size_is_gather != (int)nb_dofs_row)
      SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
               "data inconsistency %d != %d", size_is_gather, nb_dofs_row);
 
    CHKERR ISGetSize(is_num, &size_is_num);
    if (size_is_num != (int)nb_dofs_row)
      SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
               "data inconsistency %d != %d", size_is_num, nb_dofs_row);
 
    bool square_matrix = false;
    if (p_miit->numeredRowDofsPtr == p_miit->numeredColDofsPtr)
      square_matrix = true;
 
    // if (!square_matrix) {
    //   // FIXME: This is for back compatibility, if deprecate interface
    //   function
    //   // build interfaces is removed, this part of the code will be obsolete
    //   auto mit_row = p_miit->numeredRowDofsPtr->get<Idx_mi_tag>().begin();
    //   auto hi_mit_row = p_miit->numeredRowDofsPtr->get<Idx_mi_tag>().end();
    //   auto mit_col = p_miit->numeredColDofsPtr->get<Idx_mi_tag>().begin();
    //   auto hi_mit_col = p_miit->numeredColDofsPtr->get<Idx_mi_tag>().end();
    //   for (; mit_row != hi_mit_row; mit_row++, mit_col++) {
    //     if (mit_col == hi_mit_col) {
    //       SETERRQ(
    //           PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
    //           "check finite element definition, nb. of rows is not equal to "
    //           "number for columns");
    //     }
    //     if (mit_row->get()->getLocalUniqueId() !=
    //         mit_col->get()->getLocalUniqueId()) {
    //       SETERRQ(
    //           PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
    //           "check finite element definition, nb. of rows is not equal to "
    //           "number for columns");
    //     }
    //   }
    // }
 
    auto number_dofs = [&](auto &dofs_idx, auto &counter) {
      MoFEMFunctionBegin;
      for (auto miit_dofs_row = dofs_idx.begin();
           miit_dofs_row != dofs_idx.end(); miit_dofs_row++) {
        const int part = part_number[(*miit_dofs_row)->dofIdx];
        if (part == (unsigned int)m_field.get_comm_rank()) {
          const bool success = dofs_idx.modify(
              miit_dofs_row,
              NumeredDofEntity_part_and_indices_change(
                  part, petsc_idx[(*miit_dofs_row)->dofIdx], counter++));
          if (!success) {
            SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
          }
        } else {
          const bool success = dofs_idx.modify(
              miit_dofs_row, NumeredDofEntity_part_and_glob_idx_change(
                                 part, petsc_idx[(*miit_dofs_row)->dofIdx]));
          if (!success) {
            SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
          }
        }
      }
      MoFEMFunctionReturn(0);
    };
 
    // Set petsc global indices
    auto &dofs_row_by_idx_no_const = const_cast<NumeredDofEntitysByIdx &>(
        p_miit->numeredRowDofsPtr->get<Idx_mi_tag>());
    int &nb_row_local_dofs = p_miit->nbLocDofsRow;
    int &nb_row_ghost_dofs = p_miit->nbGhostDofsRow;
    nb_row_local_dofs = 0;
    nb_row_ghost_dofs = 0;
 
    CHKERR number_dofs(dofs_row_by_idx_no_const, nb_row_local_dofs);
 
    int &nb_col_local_dofs = p_miit->nbLocDofsCol;
    int &nb_col_ghost_dofs = p_miit->nbGhostDofsCol;
    if (square_matrix) {
      nb_col_local_dofs = nb_row_local_dofs;
      nb_col_ghost_dofs = nb_row_ghost_dofs;
    } else {
      NumeredDofEntitysByIdx &dofs_col_by_idx_no_const =
          const_cast<NumeredDofEntitysByIdx &>(
              p_miit->numeredColDofsPtr->get<Idx_mi_tag>());
      nb_col_local_dofs = 0;
      nb_col_ghost_dofs = 0;
      CHKERR number_dofs(dofs_col_by_idx_no_const, nb_col_local_dofs);
    }
 
    CHKERR ISRestoreIndices(is_gather, &part_number);
    CHKERR ISRestoreIndices(is_gather_num, &petsc_idx);
    CHKERR ISDestroy(&is_num);
    CHKERR ISDestroy(&is_gather_num);
    CHKERR ISDestroy(&is_gather);
    CHKERR ISDestroy(&is);
    CHKERR MatPartitioningDestroy(&part);
    CHKERR MatDestroy(&Adj);
    CHKERR printPartitionedProblem(&*p_miit, verb);
  } else {
 
    auto number_dofs = [&](auto &dof_idx, auto &counter) {
      MoFEMFunctionBeginHot;
      for (auto miit_dofs_row = dof_idx.begin(); miit_dofs_row != dof_idx.end();
           miit_dofs_row++) {
        const bool success = dof_idx.modify(
            miit_dofs_row,
            NumeredDofEntity_part_and_indices_change(0, counter, counter));
        ++counter;
        if (!success) {
          SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        }
      }
      MoFEMFunctionReturnHot(0);
    };
 
    auto &dofs_row_by_idx_no_const = const_cast<NumeredDofEntitysByIdx &>(
        p_miit->numeredRowDofsPtr->get<Idx_mi_tag>());
    int &nb_row_local_dofs = p_miit->nbLocDofsRow;
    int &nb_row_ghost_dofs = p_miit->nbGhostDofsRow;
    nb_row_local_dofs = 0;
    nb_row_ghost_dofs = 0;
 
    CHKERR number_dofs(dofs_row_by_idx_no_const, nb_row_local_dofs);
 
    bool square_matrix = false;
    if (p_miit->numeredRowDofsPtr == p_miit->numeredColDofsPtr)
      square_matrix = true;
 
    int &nb_col_local_dofs = p_miit->nbLocDofsCol;
    int &nb_col_ghost_dofs = p_miit->nbGhostDofsCol;
    if (square_matrix) {
      nb_col_local_dofs = nb_row_local_dofs;
      nb_col_ghost_dofs = nb_row_ghost_dofs;
    } else {
      NumeredDofEntitysByIdx &dofs_col_by_idx_no_const =
          const_cast<NumeredDofEntitysByIdx &>(
              p_miit->numeredColDofsPtr->get<Idx_mi_tag>());
      nb_col_local_dofs = 0;
      nb_col_ghost_dofs = 0;
      CHKERR number_dofs(dofs_col_by_idx_no_const, nb_col_local_dofs);
    }
  }
 
  cOre.getBuildMoFEM() |= 1 << 4;
  MoFEMFunctionReturn(0);
}

partitionSimpleProblem()

MoFEMErrorCode MoFEM::ProblemsManager::partitionSimpleProblem	(	const std::string	name,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

partition problem dofs

Partitions DOFs for sequential/simple problems where the mesh is not distributed across processors. Creates local DOF numbering and assigns ownership to processors.

Parameters

name	problem name to partition
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Examples

mofem/atom_tests/forces_and_sources_testing_edge_element.cpp, mofem/atom_tests/forces_and_sources_testing_flat_prism_element.cpp, mofem/atom_tests/hcurl_divergence_operator_2d.cpp, mofem/atom_tests/prism_elements_from_surface.cpp, mofem/atom_tests/prism_polynomial_approximation.cpp, and mofem/atom_tests/quad_polynomial_approximation.cpp.

Definition at line 1533 of file ProblemsManager.cpp.

                                                                 {
 
  MoFEM::Interface &m_field = cOre;
  auto problems_ptr = m_field.get_problems();
  ProblemManagerFunctionBegin;
 
  if (!(cOre.getBuildMoFEM() & Core::BUILD_FIELD))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "fields not build");
  if (!(cOre.getBuildMoFEM() & Core::BUILD_FE))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "FEs not build");
  if (!(cOre.getBuildMoFEM() & Core::BUILD_ADJ))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "adjacencies not build");
  if (!(cOre.getBuildMoFEM() & Core::BUILD_PROBLEM))
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "adjacencies not build");
  MOFEM_LOG("WORLD", Sev::verbose) << "Simple partition problem " << name;
 
  // find p_miit
  typedef Problem_multiIndex::index<Problem_mi_tag>::type ProblemByName;
  ProblemByName &problems_set =
      const_cast<ProblemByName &>(problems_ptr->get<Problem_mi_tag>());
  ProblemByName::iterator p_miit = problems_set.find(name);
  if (p_miit == problems_set.end()) {
    SETERRQ(PETSC_COMM_SELF, 1,
             "problem < %s > is not found (top tip: check spelling)",
             name.c_str());
  }
  typedef boost::multi_index::index<NumeredDofEntity_multiIndex,
                                    Idx_mi_tag>::type NumeredDofEntitysByIdx;
  NumeredDofEntitysByIdx &dofs_row_by_idx =
      p_miit->numeredRowDofsPtr->get<Idx_mi_tag>();
  NumeredDofEntitysByIdx &dofs_col_by_idx =
      p_miit->numeredColDofsPtr->get<Idx_mi_tag>();
  boost::multi_index::index<NumeredDofEntity_multiIndex,
                            Idx_mi_tag>::type::iterator miit_row,
      hi_miit_row;
  boost::multi_index::index<NumeredDofEntity_multiIndex,
                            Idx_mi_tag>::type::iterator miit_col,
      hi_miit_col;
  DofIdx &nb_row_local_dofs = p_miit->nbLocDofsRow;
  DofIdx &nb_row_ghost_dofs = p_miit->nbGhostDofsRow;
  nb_row_local_dofs = 0;
  nb_row_ghost_dofs = 0;
  DofIdx &nb_col_local_dofs = p_miit->nbLocDofsCol;
  DofIdx &nb_col_ghost_dofs = p_miit->nbGhostDofsCol;
  nb_col_local_dofs = 0;
  nb_col_ghost_dofs = 0;
 
  bool square_matrix = false;
  if (p_miit->numeredRowDofsPtr == p_miit->numeredColDofsPtr) {
    square_matrix = true;
  }
 
  // get row range of local indices
  PetscLayout layout_row;
  const int *ranges_row;
 
  DofIdx nb_dofs_row = dofs_row_by_idx.size();
  CHKERR PetscLayoutCreate(m_field.get_comm(), &layout_row);
  CHKERR PetscLayoutSetBlockSize(layout_row, 1);
  CHKERR PetscLayoutSetSize(layout_row, nb_dofs_row);
  CHKERR PetscLayoutSetUp(layout_row);
  CHKERR PetscLayoutGetRanges(layout_row, &ranges_row);
  // get col range of local indices
  PetscLayout layout_col;
  const int *ranges_col;
  if (!square_matrix) {
    DofIdx nb_dofs_col = dofs_col_by_idx.size();
    CHKERR PetscLayoutCreate(m_field.get_comm(), &layout_col);
    CHKERR PetscLayoutSetBlockSize(layout_col, 1);
    CHKERR PetscLayoutSetSize(layout_col, nb_dofs_col);
    CHKERR PetscLayoutSetUp(layout_col);
    CHKERR PetscLayoutGetRanges(layout_col, &ranges_col);
  }
  for (unsigned int part = 0; part < (unsigned int)m_field.get_comm_size();
       part++) {
    miit_row = dofs_row_by_idx.lower_bound(ranges_row[part]);
    hi_miit_row = dofs_row_by_idx.lower_bound(ranges_row[part + 1]);
    if (std::distance(miit_row, hi_miit_row) !=
        ranges_row[part + 1] - ranges_row[part]) {
      SETERRQ(
          PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
          "data inconsistency, std::distance(miit_row,hi_miit_row) != rend - "
          "rstart (%ld != %d - %d = %d) ",
          std::distance(miit_row, hi_miit_row), ranges_row[part + 1],
          ranges_row[part], ranges_row[part + 1] - ranges_row[part]);
    }
    // loop rows
    for (; miit_row != hi_miit_row; miit_row++) {
      bool success = dofs_row_by_idx.modify(
          miit_row,
          NumeredDofEntity_part_and_glob_idx_change(part, (*miit_row)->dofIdx));
      if (!success)
        SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                "modification unsuccessful");
      if (part == (unsigned int)m_field.get_comm_rank()) {
        success = dofs_row_by_idx.modify(
            miit_row, NumeredDofEntity_local_idx_change(nb_row_local_dofs++));
        if (!success)
          SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
      }
    }
    if (!square_matrix) {
      miit_col = dofs_col_by_idx.lower_bound(ranges_col[part]);
      hi_miit_col = dofs_col_by_idx.lower_bound(ranges_col[part + 1]);
      if (std::distance(miit_col, hi_miit_col) !=
          ranges_col[part + 1] - ranges_col[part]) {
        SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ,
                 "data inconsistency, std::distance(miit_col,hi_miit_col) != "
                 "rend - "
                 "rstart (%ld != %d - %d = %d) ",
                 std::distance(miit_col, hi_miit_col), ranges_col[part + 1],
                 ranges_col[part], ranges_col[part + 1] - ranges_col[part]);
      }
      // loop cols
      for (; miit_col != hi_miit_col; miit_col++) {
        bool success = dofs_col_by_idx.modify(
            miit_col, NumeredDofEntity_part_and_glob_idx_change(
                          part, (*miit_col)->dofIdx));
        if (!success)
          SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                  "modification unsuccessful");
        if (part == (unsigned int)m_field.get_comm_rank()) {
          success = dofs_col_by_idx.modify(
              miit_col, NumeredDofEntity_local_idx_change(nb_col_local_dofs++));
          if (!success)
            SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                    "modification unsuccessful");
        }
      }
    }
  }
  CHKERR PetscLayoutDestroy(&layout_row);
  if (!square_matrix) {
    CHKERR PetscLayoutDestroy(&layout_col);
  }
  if (square_matrix) {
    nb_col_local_dofs = nb_row_local_dofs;
    nb_col_ghost_dofs = nb_row_ghost_dofs;
  }
  CHKERR printPartitionedProblem(&*p_miit, verb);
  cOre.getBuildMoFEM() |= Core::PARTITION_PROBLEM;
  MoFEMFunctionReturn(0);
}

printPartitionedProblem()

MoFEMErrorCode MoFEM::ProblemsManager::printPartitionedProblem	(	const Problem *	problem_ptr,
		int	verb = VERBOSE
	)

#include <src/interfaces/ProblemsManager.hpp>

Print partition information for debugging.

Outputs detailed information about how DOFs and finite elements are distributed across processors for the given problem.

Parameters

problem_ptr	pointer to the problem structure
verb	verbosity level

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 2061 of file ProblemsManager.cpp.

                                                                             {
  MoFEM::Interface &m_field = cOre;
  ProblemManagerFunctionBegin;
 
  if (verb > QUIET) {
 
    MOFEM_LOG("SYNC", Sev::inform)
        << problem_ptr->getName() << " Nb. local dof "
        << problem_ptr->getNbLocalDofsRow() << " by "
        << problem_ptr->getNbLocalDofsCol() << " nb global dofs "
        << problem_ptr->getNbDofsRow() << " by " << problem_ptr->getNbDofsCol();
 
    MOFEM_LOG_SYNCHRONISE(m_field.get_comm())
  }
 
  MoFEMFunctionReturn(0);
}

removeDofs()

MoFEMErrorCode MoFEM::ProblemsManager::removeDofs	(	const std::string	problem_name,
		RowColData	rc,
		std::vector< boost::weak_ptr< NumeredDofEntity > > &	vec_dof_view,
		int	verb = VERBOSE,
		const bool	debug = false
	)

#include <src/interfaces/ProblemsManager.hpp>

Remove DOFs from problem on broken space.

Removes specified DOFs from the problem for broken (discontinuous) spaces. The DOFs are marked as inactive by setting their indices to -1, which causes them to be skipped during assembly operations.

Parameters

problem_name	name of the problem
rc	row or column data specification
vec_dof_view	vector of DOF entities to remove
verb	verbosity level
debug	enable debug output for inconsistency checking

Returns

MoFEMErrorCode Error code indicating success or failure

Definition at line 2719 of file ProblemsManager.cpp.

                      {
 
  MoFEM::Interface &m_field = cOre;
  ProblemManagerFunctionBegin;
 
  switch (rc) {
  case ROW:
  case COL:
    break;
  default:
    SETERRQ(PETSC_COMM_SELF, MOFEM_IMPOSSIBLE_CASE, "Should be row or column");
  }
 
  const Problem *prb_ptr;
  CHKERR m_field.get_problem(problem_name, &prb_ptr);
 
  decltype(prb_ptr->numeredRowDofsPtr) numered_dofs[2] = {
      prb_ptr->numeredRowDofsPtr, nullptr};
  if (prb_ptr->numeredRowDofsPtr != prb_ptr->numeredColDofsPtr)
    numered_dofs[1] = prb_ptr->numeredColDofsPtr;
 
  int *nbdof_ptr[] = {&prb_ptr->nbDofsRow, &prb_ptr->nbDofsCol};
  int *local_nbdof_ptr[] = {&prb_ptr->nbLocDofsRow, &prb_ptr->nbLocDofsCol};
  int *ghost_nbdof_ptr[] = {&prb_ptr->nbGhostDofsRow, &prb_ptr->nbGhostDofsCol};
 
  const int nb_init_row_dofs = prb_ptr->getNbDofsRow();
  const int nb_init_col_dofs = prb_ptr->getNbDofsCol();
  const int nb_init_loc_row_dofs = prb_ptr->getNbLocalDofsRow();
  const int nb_init_ghost_row_dofs = prb_ptr->getNbGhostDofsRow();
  const int nb_init_ghost_col_dofs = prb_ptr->getNbGhostDofsCol();
 
  if (numered_dofs[rc]) {
 
    if (verb >= NOISY)
      MOFEM_LOG_C("SYNC", Sev::noisy,
                  "Number of DOFs in multi-index %d and to delete %d\n",
                  numered_dofs[rc]->size(), vec_dof_view.size());
 
    // erase dofs from problem
    for (auto weak_dit : vec_dof_view)
      if (auto dit = weak_dit.lock()) {
        numered_dofs[rc]->erase(dit->getLocalUniqueId());
      }
 
    if (verb >= NOISY)
      MOFEM_LOG_C("SYNC", Sev::noisy,
                  "Number of DOFs in multi-index after delete %d\n",
                  numered_dofs[rc]->size());
 
    // get current number of ghost dofs
    int nb_local_dofs = 0;
    int nb_ghost_dofs = 0;
    for (auto dit = numered_dofs[rc]->get<PetscLocalIdx_mi_tag>().begin();
         dit != numered_dofs[rc]->get<PetscLocalIdx_mi_tag>().end(); ++dit) {
      if ((*dit)->getPetscLocalDofIdx() >= 0 &&
          (*dit)->getPetscLocalDofIdx() < *(local_nbdof_ptr[rc]))
        ++nb_local_dofs;
      else if ((*dit)->getPetscLocalDofIdx() >= *(local_nbdof_ptr[rc]))
        ++nb_ghost_dofs;
      else
        SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
                 "Impossible case. You could run problem on no distributed "
                 "mesh. That is not implemented. Dof local index is %d",
                 (*dit)->getPetscLocalDofIdx());
    }
 
    // get indices
    auto get_indices_by_tag = [&](auto tag, auto &indices, bool only_local) {
      const int nb_dofs = numered_dofs[rc]->size();
      indices.clear();
      indices.reserve(nb_dofs);
      for (auto dit = numered_dofs[rc]->get<decltype(tag)>().begin();
           dit != numered_dofs[rc]->get<decltype(tag)>().end(); ++dit) {
        bool add = true;
        if (only_local) {
          if ((*dit)->getPetscLocalDofIdx() < 0 ||
              (*dit)->getPetscLocalDofIdx() >= *(local_nbdof_ptr[rc])) {
            add = false;
          }
        }
        if (add)
          indices.push_back(decltype(tag)::get_index(dit));
      }
    };
 
    auto get_indices_by_uid = [&](auto tag, auto &indices) {
      const int nb_dofs = numered_dofs[rc]->size();
      indices.clear();
      indices.reserve(nb_dofs);
      for (auto dit = numered_dofs[rc]->begin(); dit != numered_dofs[rc]->end();
           ++dit)
        indices.push_back(decltype(tag)::get_index(dit));
    };
 
    auto get_sub_ao = [&](auto sub_data) {
      if (rc == 0) {
        return sub_data->getSmartRowMap();
      } else {
        return sub_data->getSmartColMap();
      }
    };
 
    auto set_sub_is_and_ao = [&rc, &prb_ptr](auto sub_data, auto is, auto ao) {
      if (rc == ROW) {
        sub_data->rowIs = is;
        sub_data->rowMap = ao;
        sub_data->colIs = is; // if square problem col is equal to row
        sub_data->colMap = ao;
      } else {
        sub_data->colIs = is;
        sub_data->colMap = ao;
      }
    };
 
    auto apply_symmetry = [&rc, &prb_ptr](auto sub_data) {
      if (rc == ROW) {
        if (prb_ptr->numeredRowDofsPtr == prb_ptr->numeredColDofsPtr) {
          sub_data->colIs = sub_data->getSmartRowIs();
          sub_data->colMap = sub_data->getSmartRowMap();
        }
      }
    };
 
    auto concatenate_dofs = [&](auto tag, auto &indices,
                                const auto local_only) {
      MoFEMFunctionBegin;
      get_indices_by_tag(tag, indices, local_only);
 
      SmartPetscObj<AO> ao;
      // Create AO from app indices (i.e. old), to pestc indices (new after
      // remove)
      if (local_only)
        ao = createAOMapping(m_field.get_comm(), indices.size(),
                             &*indices.begin(), PETSC_NULLPTR);
      else
        ao = createAOMapping(PETSC_COMM_SELF, indices.size(), &*indices.begin(),
                             PETSC_NULLPTR);
 
      // Set mapping to sub dm data
      if (local_only) {
        if (auto sub_data = prb_ptr->getSubData()) {
          // create is and then map it to main problem of sub-problem
          auto sub_is = createISGeneral(m_field.get_comm(), indices.size(),
                                        &*indices.begin(), PETSC_COPY_VALUES);
          // get old app, i.e. oroginal befor sub indices, and ao, from app,
          // to petsc sub indices.
          auto sub_ao = get_sub_ao(sub_data);
          CHKERR AOPetscToApplicationIS(sub_ao, sub_is);
          sub_ao = createAOMappingIS(sub_is, PETSC_NULLPTR);
          // set new sub ao
          set_sub_is_and_ao(sub_data, sub_is, sub_ao);
          apply_symmetry(sub_data);
        } else {
          // create sub data
          prb_ptr->getSubData() = boost::make_shared<Problem::SubProblemData>();
          auto sub_is = createISGeneral(m_field.get_comm(), indices.size(),
                                        &*indices.begin(), PETSC_COPY_VALUES);
          // set sub is ao
          set_sub_is_and_ao(prb_ptr->getSubData(), sub_is, ao);
          apply_symmetry(prb_ptr->getSubData());
        }
      }
 
      get_indices_by_uid(tag, indices);
      CHKERR AOApplicationToPetsc(ao, indices.size(), &*indices.begin());
 
      MoFEMFunctionReturn(0);
    };
 
    // set indices index
    auto set_concatenated_indices = [&]() {
      std::vector<int> global_indices;
      std::vector<int> local_indices;
      MoFEMFunctionBegin;
      CHKERR concatenate_dofs(PetscGlobalIdx_mi_tag(), global_indices, true);
      CHKERR concatenate_dofs(PetscLocalIdx_mi_tag(), local_indices, false);
      auto gi = global_indices.begin();
      auto li = local_indices.begin();
      for (auto dit = numered_dofs[rc]->begin(); dit != numered_dofs[rc]->end();
           ++dit) {
        auto mod = NumeredDofEntity_part_and_all_indices_change(
            (*dit)->getPart(), (*dit)->getDofIdx(), *gi, *li);
        bool success = numered_dofs[rc]->modify(dit, mod);
        if (!success)
          SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                  "can not set negative indices");
        ++gi;
        ++li;
      }
      MoFEMFunctionReturn(0);
    };
    CHKERR set_concatenated_indices();
 
    MPI_Allreduce(&nb_local_dofs, nbdof_ptr[rc], 1, MPI_INT, MPI_SUM,
                  m_field.get_comm());
    *(local_nbdof_ptr[rc]) = nb_local_dofs;
    *(ghost_nbdof_ptr[rc]) = nb_ghost_dofs;
 
    if (debug)
      for (auto dof : (*numered_dofs[rc])) {
        if (dof->getPetscGlobalDofIdx() < 0) {
          SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                  "Negative global idx");
        }
        if (dof->getPetscLocalDofIdx() < 0) {
          SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                  "Negative local idx");
        }
      }
 
  } else {
 
    *(nbdof_ptr[1]) = *(nbdof_ptr[0]);
    *(local_nbdof_ptr[1]) = *(local_nbdof_ptr[0]);
    *(ghost_nbdof_ptr[1]) = *(ghost_nbdof_ptr[0]);
  }
 
  if (verb > QUIET) {
    MOFEM_LOG_C(
        "WORLD", Sev::inform,
        "Removed DOFs from problem %s dofs [%d / %d (before %d / %d) global]",
        prb_ptr->getName().c_str(), prb_ptr->getNbDofsRow(),
        prb_ptr->getNbDofsCol(), nb_init_row_dofs, nb_init_col_dofs);
    MOFEM_LOG_C("SYNC", Sev::verbose,
                "Removed DOFs from problem %s dofs [ %d / %d  "
                "(before %d / %d) local, %d / %d (before %d / %d)]",
                prb_ptr->getName().c_str(), prb_ptr->getNbLocalDofsRow(),
                prb_ptr->getNbLocalDofsCol(), nb_init_loc_row_dofs,
                nb_init_loc_row_dofs, prb_ptr->getNbGhostDofsRow(),
                prb_ptr->getNbGhostDofsCol(), nb_init_ghost_row_dofs,
                nb_init_ghost_col_dofs);
    MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::verbose);
  }
 
  MoFEMFunctionReturn(0);
}

removeDofsOnEntities() [1/2]

MoFEMErrorCode MoFEM::ProblemsManager::removeDofsOnEntities	(	const std::string	problem_name,
		const std::string	field_name,
		const BitRefLevel	bit_ref_level,
		const BitRefLevel	bit_ref_mask,
		Range *	ents_ptr = nullptr,
		const int	lo_coeff = 0,
		const int	hi_coeff = MAX_DOFS_ON_ENTITY,
		const int	lo_order = 0,
		const int	hi_order = 100,
		int	verb = VERBOSE,
		const bool	debug = false
	)

#include <src/interfaces/ProblemsManager.hpp>

Remove DOFs from problem by bit ref level.

See for more detail other implementation for removeDofsOnEntities.

Parameters

problem_name	name of the problem
field_name	name of the field
bit_ref_level	bit ref level on which DOFs are removed
bit_ref_mask	bit ref mask on which DOFs are removed
ents_ptr	filter entities with given bit and mask
lo_coeff	low dof coefficient (rank)
hi_coeff	high dof coefficient (rank)
verb	verbosity level
debug	to debug and seek for inconsistencies set to true

Returns

MoFEMErrorCode

Definition at line 3499 of file ProblemsManager.cpp.

                                                    {
  MoFEM::Interface &m_field = cOre;
  MoFEMFunctionBegin;
 
  auto bit_manager = m_field.getInterface<BitRefManager>();
 
  Range ents;
  if (ents_ptr) {
    ents = *ents_ptr;
    CHKERR bit_manager->filterEntitiesByRefLevel(bit_ref_level, bit_ref_mask,
                                                 ents, verb);
  } else {
    CHKERR bit_manager->getEntitiesByRefLevel(bit_ref_level, bit_ref_mask, ents,
                                              verb);
  }
 
  CHKERR removeDofsOnEntities(problem_name, field_name, ents, lo_coeff,
                              hi_coeff, lo_order, hi_order, verb, debug);
 
  MoFEMFunctionReturn(0);
}

removeDofsOnEntities() [2/2]

MoFEMErrorCode MoFEM::ProblemsManager::removeDofsOnEntities	(	const std::string	problem_name,
		const std::string	field_name,
		const Range	ents,
		const int	lo_coeff = 0,
		const int	hi_coeff = MAX_DOFS_ON_ENTITY,
		const int	lo_order = 0,
		const int	hi_order = 100,
		int	verb = VERBOSE,
		const bool	debug = false
	)

#include <src/interfaces/ProblemsManager.hpp>

Remove DOFs from problem.

Remove DOFs from problem which are on entities on the given range and given field name. On the finite element level, DOFs can be still accessed however local PETSc indices and global PETSc indices are marked with the index -1.

Note

If the index is marked -1 it is not assembled and dropped by VecSetValues and MatSetValues.

Todo:

Not yet implemented update for AO maps and IS ranges if removed entities in composite problem or sub-problem

Parameters

problem_name	name of the problem
field_name	name of the field
ents	entities on which DOFs are removed
lo_coeff	low dof coefficient (rank)
hi_coeff	high dof coefficient (rank)
verb	verbosity level
debug	to debug and seek for inconsistencies set to true

Returns

MoFEMErrorCode

Examples

mofem/atom_tests/hanging_node_approx.cpp, mofem/atom_tests/remove_entities_from_problem.cpp, and mofem/tutorials/clx-0/helmholtz.cpp.

Definition at line 2959 of file ProblemsManager.cpp.

                                                                        {
 
  MoFEM::Interface &m_field = cOre;
  ProblemManagerFunctionBegin;
 
  const Problem *prb_ptr;
  CHKERR m_field.get_problem(problem_name, &prb_ptr);
 
  decltype(prb_ptr->numeredRowDofsPtr) numered_dofs[2] = {
      prb_ptr->numeredRowDofsPtr, nullptr};
  if (prb_ptr->numeredRowDofsPtr != prb_ptr->numeredColDofsPtr)
    numered_dofs[1] = prb_ptr->numeredColDofsPtr;
 
  int *nbdof_ptr[] = {&prb_ptr->nbDofsRow, &prb_ptr->nbDofsCol};
  int *local_nbdof_ptr[] = {&prb_ptr->nbLocDofsRow, &prb_ptr->nbLocDofsCol};
  int *ghost_nbdof_ptr[] = {&prb_ptr->nbGhostDofsRow, &prb_ptr->nbGhostDofsCol};
 
  const int nb_init_row_dofs = prb_ptr->getNbDofsRow();
  const int nb_init_col_dofs = prb_ptr->getNbDofsCol();
  const int nb_init_loc_row_dofs = prb_ptr->getNbLocalDofsRow();
  // const int nb_init_loc_col_dofs = prb_ptr->getNbLocalDofsCol();
  const int nb_init_ghost_row_dofs = prb_ptr->getNbGhostDofsRow();
  const int nb_init_ghost_col_dofs = prb_ptr->getNbGhostDofsCol();
 
  for (int s = 0; s != 2; ++s)
    if (numered_dofs[s]) {
 
      using NumeredDofEntity_it_view_multiIndex = multi_index_container<
 
          NumeredDofEntity_multiIndex::iterator, indexed_by<sequenced<>>
 
          >;
 
      const auto bit_number = m_field.get_field_bit_number(field_name);
      NumeredDofEntity_it_view_multiIndex dofs_it_view;
 
      // Set -1 to global and local dofs indices
      for (auto pit = ents.const_pair_begin(); pit != ents.const_pair_end();
           ++pit) {
        auto lo = numered_dofs[s]->get<Unique_mi_tag>().lower_bound(
            DofEntity::getLoFieldEntityUId(bit_number, pit->first));
        auto hi = numered_dofs[s]->get<Unique_mi_tag>().upper_bound(
            DofEntity::getHiFieldEntityUId(bit_number, pit->second));
 
        for (; lo != hi; ++lo)
          if ((*lo)->getDofCoeffIdx() >= lo_coeff &&
              (*lo)->getDofCoeffIdx() <= hi_coeff &&
              (*lo)->getDofOrder() >= lo_order &&
              (*lo)->getDofOrder() <= hi_order)
            dofs_it_view.emplace_back(numered_dofs[s]->project<0>(lo));
      }
 
      if (verb > QUIET) {
        for (auto &dof : dofs_it_view)
          MOFEM_LOG("SYNC", Sev::noisy) << **dof;
        MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::noisy);
      }
 
      // create weak view
      std::vector<boost::weak_ptr<NumeredDofEntity>> dofs_weak_view;
      dofs_weak_view.reserve(dofs_it_view.size());
      for (auto dit : dofs_it_view)
        dofs_weak_view.push_back(*dit);
 
      if (verb >= NOISY)
        MOFEM_LOG_C("SYNC", Sev::noisy,
                    "Number of DOFs in multi-index %d and to delete %d\n",
                    numered_dofs[s]->size(), dofs_it_view.size());
 
      // erase dofs from problem
      for (auto weak_dit : dofs_weak_view)
        if (auto dit = weak_dit.lock()) {
          numered_dofs[s]->erase(dit->getLocalUniqueId());
        }
 
      if (verb >= NOISY)
        MOFEM_LOG_C("SYNC", Sev::noisy,
                    "Number of DOFs in multi-index after delete %d\n",
                    numered_dofs[s]->size());
 
      // get current number of ghost dofs
      int nb_local_dofs = 0;
      int nb_ghost_dofs = 0;
      for (auto dit = numered_dofs[s]->get<PetscLocalIdx_mi_tag>().begin();
           dit != numered_dofs[s]->get<PetscLocalIdx_mi_tag>().end(); ++dit) {
        if ((*dit)->getPetscLocalDofIdx() >= 0 &&
            (*dit)->getPetscLocalDofIdx() < *(local_nbdof_ptr[s]))
          ++nb_local_dofs;
        else if ((*dit)->getPetscLocalDofIdx() >= *(local_nbdof_ptr[s]))
          ++nb_ghost_dofs;
        else
          SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
                   "Impossible case. You could run problem on no distributed "
                   "mesh. That is not implemented. Dof local index is %d",
                   (*dit)->getPetscLocalDofIdx());
      }
 
      // get indices
      auto get_indices_by_tag = [&](auto tag, auto &indices, bool only_local) {
        const int nb_dofs = numered_dofs[s]->size();
        indices.clear();
        indices.reserve(nb_dofs);
        for (auto dit = numered_dofs[s]->get<decltype(tag)>().begin();
             dit != numered_dofs[s]->get<decltype(tag)>().end(); ++dit) {
          bool add = true;
          if (only_local) {
            if ((*dit)->getPetscLocalDofIdx() < 0 ||
                (*dit)->getPetscLocalDofIdx() >= *(local_nbdof_ptr[s])) {
              add = false;
            }
          }
          if (add)
            indices.push_back(decltype(tag)::get_index(dit));
        }
      };
 
      auto get_indices_by_uid = [&](auto tag, auto &indices) {
        const int nb_dofs = numered_dofs[s]->size();
        indices.clear();
        indices.reserve(nb_dofs);
        for (auto dit = numered_dofs[s]->begin(); dit != numered_dofs[s]->end();
             ++dit)
          indices.push_back(decltype(tag)::get_index(dit));
      };
 
      auto get_sub_ao = [&](auto sub_data) {
        if (s == 0) {
          return sub_data->getSmartRowMap();
        } else {
          return sub_data->getSmartColMap();
        }
      };
 
      auto set_sub_is_and_ao = [&s, &prb_ptr](auto sub_data, auto is, auto ao) {
        if (s == 0) {
          sub_data->rowIs = is;
          sub_data->rowMap = ao;
          sub_data->colIs = is; // if square problem col is equal to row
          sub_data->colMap = ao;
        } else {
          sub_data->colIs = is;
          sub_data->colMap = ao;
        }
      };
 
      auto apply_symmetry = [&s, &prb_ptr](auto sub_data) {
        if (s == 0) {
          if (prb_ptr->numeredRowDofsPtr == prb_ptr->numeredColDofsPtr) {
            sub_data->colIs = sub_data->getSmartRowIs();
            sub_data->colMap = sub_data->getSmartRowMap();
          }
        }
      };
 
      auto concatenate_dofs = [&](auto tag, auto &indices,
                                  const auto local_only) {
        MoFEMFunctionBegin;
        get_indices_by_tag(tag, indices, local_only);
 
        SmartPetscObj<AO> ao;
        // Create AO from app indices (i.e. old), to pestc indices (new after
        // remove)
        if (local_only)
          ao = createAOMapping(m_field.get_comm(), indices.size(),
                               &*indices.begin(), PETSC_NULLPTR);
        else
          ao = createAOMapping(PETSC_COMM_SELF, indices.size(),
                               &*indices.begin(), PETSC_NULLPTR);
 
        // Set mapping to sub dm data
        if (local_only) {
          if (auto sub_data = prb_ptr->getSubData()) {
            // create is and then map it to main problem of sub-problem
            auto sub_is = createISGeneral(m_field.get_comm(), indices.size(),
                                          &*indices.begin(), PETSC_COPY_VALUES);
            // get old app, i.e. oroginal befor sub indices, and ao, from app,
            // to petsc sub indices.
            auto sub_ao = get_sub_ao(sub_data);
            CHKERR AOPetscToApplicationIS(sub_ao, sub_is);
            sub_ao = createAOMappingIS(sub_is, PETSC_NULLPTR);
            // set new sub ao
            set_sub_is_and_ao(sub_data, sub_is, sub_ao);
            apply_symmetry(sub_data);
          } else {
            // create sub data
            prb_ptr->getSubData() =
                boost::make_shared<Problem::SubProblemData>();
            auto sub_is = createISGeneral(m_field.get_comm(), indices.size(),
                                          &*indices.begin(), PETSC_COPY_VALUES);
            // set sub is ao
            set_sub_is_and_ao(prb_ptr->getSubData(), sub_is, ao);
            apply_symmetry(prb_ptr->getSubData());
          }
        }
 
        get_indices_by_uid(tag, indices);
        CHKERR AOApplicationToPetsc(ao, indices.size(), &*indices.begin());
 
        MoFEMFunctionReturn(0);
      };
 
      // set indices index
      auto set_concatenated_indices = [&]() {
        std::vector<int> global_indices;
        std::vector<int> local_indices;
        MoFEMFunctionBegin;
        CHKERR concatenate_dofs(PetscGlobalIdx_mi_tag(), global_indices, true);
        CHKERR concatenate_dofs(PetscLocalIdx_mi_tag(), local_indices, false);
        auto gi = global_indices.begin();
        auto li = local_indices.begin();
        for (auto dit = numered_dofs[s]->begin(); dit != numered_dofs[s]->end();
             ++dit) {
          auto mod = NumeredDofEntity_part_and_all_indices_change(
              (*dit)->getPart(), (*dit)->getDofIdx(), *gi, *li);
          bool success = numered_dofs[s]->modify(dit, mod);
          if (!success)
            SETERRQ(PETSC_COMM_SELF, MOFEM_OPERATION_UNSUCCESSFUL,
                    "can not set negative indices");
          ++gi;
          ++li;
        }
        MoFEMFunctionReturn(0);
      };
      CHKERR set_concatenated_indices();
 
      MPI_Allreduce(&nb_local_dofs, nbdof_ptr[s], 1, MPI_INT, MPI_SUM,
                    m_field.get_comm());
      *(local_nbdof_ptr[s]) = nb_local_dofs;
      *(ghost_nbdof_ptr[s]) = nb_ghost_dofs;
 
      if (debug)
        for (auto dof : (*numered_dofs[s])) {
          if (dof->getPetscGlobalDofIdx() < 0) {
            SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                    "Negative global idx");
          }
          if (dof->getPetscLocalDofIdx() < 0) {
            SETERRQ(m_field.get_comm(), MOFEM_DATA_INCONSISTENCY,
                    "Negative local idx");
          }
        }
 
    } else {
 
      *(nbdof_ptr[1]) = *(nbdof_ptr[0]);
      *(local_nbdof_ptr[1]) = *(local_nbdof_ptr[0]);
      *(ghost_nbdof_ptr[1]) = *(ghost_nbdof_ptr[0]);
    }
 
  if (verb > QUIET) {
    MOFEM_LOG_C(
        "WORLD", Sev::inform,
        "Removed DOFs from problem %s dofs [%d / %d (before %d / %d) global]",
        prb_ptr->getName().c_str(), prb_ptr->getNbDofsRow(),
        prb_ptr->getNbDofsCol(), nb_init_row_dofs, nb_init_col_dofs);
    MOFEM_LOG_C("SYNC", Sev::verbose,
                "Removed DOFs from problem %s dofs [ %d / %d  "
                "(before %d / %d) local, %d / %d (before %d / %d)]",
                prb_ptr->getName().c_str(), prb_ptr->getNbLocalDofsRow(),
                prb_ptr->getNbLocalDofsCol(), nb_init_loc_row_dofs,
                nb_init_loc_row_dofs, prb_ptr->getNbGhostDofsRow(),
                prb_ptr->getNbGhostDofsCol(), nb_init_ghost_row_dofs,
                nb_init_ghost_col_dofs);
    MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::verbose);
  }
 
  MoFEMFunctionReturn(0);
}