void VTKIO::read (const std::string& name)
{
// This is a serial-only process for now;
// the Mesh should be read on processor 0 and
// broadcast later
libmesh_assert_equal_to (MeshOutput<MeshBase>::mesh().processor_id(), 0);
// Keep track of what kinds of elements this file contains
elems_of_dimension.clear();
elems_of_dimension.resize(4, false);
#ifndef LIBMESH_HAVE_VTK
libMesh::err << "Cannot read VTK file: " << name
<< "\nYou must have VTK installed and correctly configured to read VTK meshes."
<< std::endl;
libmesh_error();
#else
// Use a typedef, because these names are just crazy
typedef vtkSmartPointer<vtkXMLUnstructuredGridReader> MyReader;
MyReader reader = MyReader::New();
// Pass the filename along to the reader
reader->SetFileName( name.c_str() );
// Force reading
reader->Update();
// read in the grid
_vtk_grid = reader->GetOutput();
// _vtk_grid->Update(); // FIXME: Necessary?
// Get a reference to the mesh
MeshBase& mesh = MeshInput<MeshBase>::mesh();
// Clear out any pre-existing data from the Mesh
mesh.clear();
// Get the number of points from the _vtk_grid object
const unsigned int vtk_num_points = static_cast<unsigned int>(_vtk_grid->GetNumberOfPoints());
// always numbered nicely??, so we can loop like this
// I'm pretty sure it is numbered nicely
for (unsigned int i=0; i<vtk_num_points; ++i)
{
// add to the id map
// and add the actual point
double * pnt = _vtk_grid->GetPoint(static_cast<vtkIdType>(i));
Point xyz(pnt[0], pnt[1], pnt[2]);
Node* newnode = mesh.add_point(xyz, i);
// Add node to the nodes vector &
// tell the MeshData object the foreign node id.
if (this->_mesh_data != NULL)
this->_mesh_data->add_foreign_node_id (newnode, i);
}
// Get the number of cells from the _vtk_grid object
const unsigned int vtk_num_cells = static_cast<unsigned int>(_vtk_grid->GetNumberOfCells());
for (unsigned int i=0; i<vtk_num_cells; ++i)
{
vtkCell* cell = _vtk_grid->GetCell(i);
Elem* elem = NULL;
switch (cell->GetCellType())
{
case VTK_LINE:
elem = new Edge2;
break;
case VTK_QUADRATIC_EDGE:
elem = new Edge3;
break;
case VTK_TRIANGLE:
elem = new Tri3();
break;
case VTK_QUADRATIC_TRIANGLE:
elem = new Tri6();
break;
case VTK_QUAD:
elem = new Quad4();
break;
case VTK_QUADRATIC_QUAD:
elem = new Quad8();
break;
#if VTK_MAJOR_VERSION > 5 || (VTK_MAJOR_VERSION == 5 && VTK_MINOR_VERSION > 0)
case VTK_BIQUADRATIC_QUAD:
elem = new Quad9();
break;
#endif
case VTK_TETRA:
elem = new Tet4();
break;
case VTK_QUADRATIC_TETRA:
elem = new Tet10();
break;
case VTK_WEDGE:
elem = new Prism6();
break;
case VTK_QUADRATIC_WEDGE:
elem = new Prism15();
break;
case VTK_BIQUADRATIC_QUADRATIC_WEDGE:
elem = new Prism18();
break;
case VTK_HEXAHEDRON:
elem = new Hex8();
break;
case VTK_QUADRATIC_HEXAHEDRON:
elem = new Hex20();
break;
case VTK_TRIQUADRATIC_HEXAHEDRON:
elem = new Hex27();
break;
case VTK_PYRAMID:
elem = new Pyramid5();
break;
default:
libMesh::err << "element type not implemented in vtkinterface " << cell->GetCellType() << std::endl;
libmesh_error();
break;
}
// get the straightforward numbering from the VTK cells
for (unsigned int j=0; j<elem->n_nodes(); ++j)
elem->set_node(j) = mesh.node_ptr(cell->GetPointId(j));
// then get the connectivity
std::vector<dof_id_type> conn;
elem->connectivity(0, VTK, conn);
// then reshuffle the nodes according to the connectivity, this
// two-time-assign would evade the definition of the vtk_mapping
for (unsigned int j=0; j<conn.size(); ++j)
elem->set_node(j) = mesh.node_ptr(conn[j]);
elem->set_id(i);
elems_of_dimension[elem->dim()] = true;
mesh.add_elem(elem);
} // end loop over VTK cells
// Set the mesh dimension to the largest encountered for an element
for (unsigned int i=0; i!=4; ++i)
if (elems_of_dimension[i])
mesh.set_mesh_dimension(i);
#if LIBMESH_DIM < 3
if (mesh.mesh_dimension() > LIBMESH_DIM)
{
libMesh::err << "Cannot open dimension " <<
mesh.mesh_dimension() <<
" mesh file when configured without " <<
mesh.mesh_dimension() << "D support." <<
std::endl;
libmesh_error();
}
#endif
#endif // LIBMESH_HAVE_VTK
}
void
CombinedCreepPlasticity::computeStress( const Elem & current_elem,
unsigned qp, const SymmElasticityTensor & elasticityTensor,
const SymmTensor & stress_old, SymmTensor & strain_increment,
SymmTensor & stress_new )
{
// Given the stretching, compute the stress increment and add it to the old stress. Also update the creep strain
// stress = stressOld + stressIncrement
// creep_strain = creep_strainOld + creep_strainIncrement
if(_t_step == 0) return;
if (_output_iteration_info == true)
{
Moose::out
<< std::endl
<< "iteration output for CombinedCreepPlasticity solve:"
<< " time=" <<_t
<< " temperature=" << _temperature[qp]
<< " int_pt=" << qp
<< std::endl;
}
// compute trial stress
stress_new = elasticityTensor * strain_increment;
stress_new += stress_old;
const SubdomainID current_block = current_elem.subdomain_id();
const std::vector<ReturnMappingModel*> & rmm( _submodels[current_block] );
const unsigned num_submodels = rmm.size();
SymmTensor inelastic_strain_increment;
SymmTensor elastic_strain_increment;
SymmTensor stress_new_last( stress_new );
Real delS(_absolute_tolerance+1);
Real first_delS(delS);
unsigned int counter(0);
while(counter < _max_its &&
delS > _absolute_tolerance &&
(delS/first_delS) > _relative_tolerance &&
(num_submodels != 1 || counter < 1))
{
elastic_strain_increment = strain_increment;
stress_new = elasticityTensor * (elastic_strain_increment - inelastic_strain_increment);
stress_new += stress_old;
for (unsigned i_rmm(0); i_rmm < num_submodels; ++i_rmm)
{
rmm[i_rmm]->computeStress( current_elem, qp, elasticityTensor, stress_old, elastic_strain_increment,
stress_new, inelastic_strain_increment );
}
// now check convergence
SymmTensor deltaS(stress_new_last - stress_new);
delS = std::sqrt(deltaS.doubleContraction(deltaS));
if (counter == 0)
{
first_delS = delS;
}
stress_new_last = stress_new;
if (_output_iteration_info == true)
{
Moose::out
<< "stress_it=" << counter
<< " rel_delS=" << (0 == first_delS ? 0 : delS/first_delS)
<< " rel_tol=" << _relative_tolerance
<< " abs_delS=" << delS
<< " abs_tol=" << _absolute_tolerance
<< std::endl;
}
++counter;
}
if(counter == _max_its &&
delS > _absolute_tolerance &&
(delS/first_delS) > _relative_tolerance)
{
mooseError("Max stress iteration hit during CombinedCreepPlasticity solve!");
}
strain_increment = elastic_strain_increment;
}
bool MeshRefinement::eliminate_unrefined_patches ()
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
// First assume that we'll have to flag this element for both h
// and p refinement, then change our minds if we see any
// neighbors that are as coarse or coarser than us.
bool h_flag_me = true,
p_flag_me = true;
// Skip the element if it is already fully flagged for refinement
if (elem->p_refinement_flag() == Elem::REFINE)
p_flag_me = false;
if (elem->refinement_flag() == Elem::REFINE)
{
h_flag_me = false;
if (!p_flag_me)
continue;
}
// Test the parent if that is already flagged for coarsening
else if (elem->refinement_flag() == Elem::COARSEN)
{
libmesh_assert(elem->parent());
elem = elem->parent();
// FIXME - this doesn't seem right - RHS
if (elem->refinement_flag() != Elem::COARSEN_INACTIVE)
continue;
p_flag_me = false;
}
const unsigned int my_level = elem->level();
int my_p_adjustment = 0;
if (elem->p_refinement_flag() == Elem::REFINE)
my_p_adjustment = 1;
else if (elem->p_refinement_flag() == Elem::COARSEN)
{
libmesh_assert_greater (elem->p_level(), 0);
my_p_adjustment = -1;
}
const unsigned int my_new_p_level = elem->p_level() +
my_p_adjustment;
// Check all the element neighbors
for (unsigned int n=0; n<elem->n_neighbors(); n++)
{
const Elem *neighbor = elem->neighbor(n);
// Quit if the element is on a local boundary
if (neighbor == NULL || neighbor == remote_elem)
{
h_flag_me = false;
p_flag_me = false;
break;
}
// if the neighbor will be equally or less refined than
// we are, then we will not become an unrefined island.
// So if we are still considering h refinement:
if (h_flag_me &&
// If our neighbor is already at a lower level,
// it can't end up at a higher level even if it
// is flagged for refinement once
((neighbor->level() < my_level) ||
// If our neighbor is at the same level but isn't
// flagged for refinement, it won't end up at a
// higher level
((neighbor->active()) &&
(neighbor->refinement_flag() != Elem::REFINE)) ||
// If our neighbor is currently more refined but is
// a parent flagged for coarsening, it will end up
// at the same level.
(neighbor->refinement_flag() == Elem::COARSEN_INACTIVE)))
{
// We've proven we won't become an unrefined island,
// so don't h refine to avoid that.
h_flag_me = false;
// If we've also proven we don't need to p refine,
// we don't need to check more neighbors
if (!p_flag_me)
break;
}
if (p_flag_me)
{
// if active neighbors will have a p level
// equal to or lower than ours, then we do not need to p
// refine ourselves.
if (neighbor->active())
{
int p_adjustment = 0;
if (neighbor->p_refinement_flag() == Elem::REFINE)
p_adjustment = 1;
else if (neighbor->p_refinement_flag() == Elem::COARSEN)
{
libmesh_assert_greater (neighbor->p_level(), 0);
p_adjustment = -1;
}
if (my_new_p_level >= neighbor->p_level() + p_adjustment)
{
p_flag_me = false;
if (!h_flag_me)
break;
}
}
// If we have inactive neighbors, we need to
// test all their active descendants which neighbor us
else if (neighbor->ancestor())
{
if (neighbor->min_new_p_level_by_neighbor(elem,
my_new_p_level + 2) <= my_new_p_level)
{
p_flag_me = false;
if (!h_flag_me)
break;
}
}
}
}
if (h_flag_me)
{
// Parents that would create islands should no longer
// coarsen
if (elem->refinement_flag() == Elem::COARSEN_INACTIVE)
{
for (unsigned int c=0; c<elem->n_children(); c++)
{
libmesh_assert_equal_to (elem->child(c)->refinement_flag(),
Elem::COARSEN);
elem->child(c)->set_refinement_flag(Elem::DO_NOTHING);
}
elem->set_refinement_flag(Elem::INACTIVE);
}
else
elem->set_refinement_flag(Elem::REFINE);
flags_changed = true;
}
if (p_flag_me)
{
if (elem->p_refinement_flag() == Elem::COARSEN)
elem->set_p_refinement_flag(Elem::DO_NOTHING);
else
elem->set_p_refinement_flag(Elem::REFINE);
flags_changed = true;
}
}
// If flags changed on any processor then they changed globally
CommWorld.max(flags_changed);
return flags_changed;
}
void MeshBase::detect_interior_parents()
{
// This requires an inspection on every processor
parallel_object_only();
// Check if the mesh contains mixed dimensions. If so, then set interior parents, otherwise return.
if (this->elem_dimensions().size() == 1)
return;
//This map will be used to set interior parents
LIBMESH_BEST_UNORDERED_MAP<dof_id_type, std::vector<dof_id_type> > node_to_elem;
const_element_iterator el = this->active_elements_begin();
const_element_iterator end = this->active_elements_end();
for (; el!=end; ++el)
{
const Elem * elem = *el;
// Populating the node_to_elem map, same as MeshTools::build_nodes_to_elem_map
for (unsigned int n=0; n<elem->n_vertices(); n++)
{
libmesh_assert_less (elem->id(), this->max_elem_id());
node_to_elem[elem->node(n)].push_back(elem->id());
}
}
// Automatically set interior parents
el = this->elements_begin();
for (; el!=end; ++el)
{
Elem * element = *el;
// Ignore an 3D element or an element that already has an interior parent
if (element->dim()>=LIBMESH_DIM || element->interior_parent())
continue;
// Start by generating a SET of elements that are dim+1 to the current
// element at each vertex of the current element, thus ignoring interior nodes.
// If one of the SET of elements is empty, then we will not have an interior parent
// since an interior parent must be connected to all vertices of the current element
std::vector< std::set<dof_id_type> > neighbors( element->n_vertices() );
bool found_interior_parents = false;
for (dof_id_type n=0; n < element->n_vertices(); n++)
{
std::vector<dof_id_type> & element_ids = node_to_elem[element->node(n)];
for (std::vector<dof_id_type>::iterator e_it = element_ids.begin();
e_it != element_ids.end(); e_it++)
{
dof_id_type eid = *e_it;
if (this->elem(eid)->dim() == element->dim()+1)
neighbors[n].insert(eid);
}
if (neighbors[n].size()>0)
{
found_interior_parents = true;
}
else
{
// We have found an empty set, no reason to continue
// Ensure we set this flag to false before the break since it could have
// been set to true for previous vertex
found_interior_parents = false;
break;
}
}
// If we have successfully generated a set of elements for each vertex, we will compare
// the set for vertex 0 will the sets for the vertices until we find a id that exists in
// all sets. If found, this is our an interior parent id. The interior parent id found
// will be the lowest element id if there is potential for multiple interior parents.
if (found_interior_parents)
{
std::set<dof_id_type> & neighbors_0 = neighbors[0];
for (std::set<dof_id_type>::iterator e_it = neighbors_0.begin();
e_it != neighbors_0.end(); e_it++)
{
found_interior_parents=false;
dof_id_type interior_parent_id = *e_it;
for (dof_id_type n=1; n < element->n_vertices(); n++)
{
if (neighbors[n].find(interior_parent_id)!=neighbors[n].end())
{
found_interior_parents=true;
}
else
{
found_interior_parents=false;
break;
}
}
if (found_interior_parents)
{
element->set_interior_parent(this->elem(interior_parent_id));
break;
}
}
}
}
}
void Elem::coarsen()
{
libmesh_assert_equal_to (this->refinement_flag(), Elem::COARSEN_INACTIVE);
libmesh_assert (!this->active());
// We no longer delete children until MeshRefinement::contract()
// delete [] _children;
// _children = NULL;
unsigned int parent_p_level = 0;
// re-compute hanging node nodal locations
for (unsigned int c=0; c<this->n_children(); c++)
{
Elem *mychild = this->child(c);
if (mychild == remote_elem)
continue;
for (unsigned int nc=0; nc<mychild->n_nodes(); nc++)
{
Point new_pos;
bool calculated_new_pos = false;
for (unsigned int n=0; n<this->n_nodes(); n++)
{
// The value from the embedding matrix
const float em_val = this->embedding_matrix(c,nc,n);
// The node location is somewhere between existing vertices
if ((em_val != 0.) && (em_val != 1.))
{
new_pos.add_scaled (this->point(n), em_val);
calculated_new_pos = true;
}
}
if(calculated_new_pos)
{
//Move the existing node back into it's original location
for(unsigned int i=0; i<LIBMESH_DIM; i++)
{
Point & child_node = *(mychild->get_node(nc));
child_node(i)=new_pos(i);
}
}
}
}
for (unsigned int c=0; c<this->n_children(); c++)
{
Elem *mychild = this->child(c);
if (mychild == remote_elem)
continue;
libmesh_assert_equal_to (mychild->refinement_flag(), Elem::COARSEN);
mychild->set_refinement_flag(Elem::INACTIVE);
if (mychild->p_level() > parent_p_level)
parent_p_level = mychild->p_level();
}
this->set_refinement_flag(Elem::JUST_COARSENED);
this->set_p_level(parent_p_level);
libmesh_assert (this->active());
}
// ------------------------------------------------------------
// MetisPartitioner implementation
void MetisPartitioner::_do_partition (MeshBase& mesh,
const unsigned int n_pieces)
{
libmesh_assert_greater (n_pieces, 0);
libmesh_assert (mesh.is_serial());
// Check for an easy return
if (n_pieces == 1)
{
this->single_partition (mesh);
return;
}
// What to do if the Metis library IS NOT present
#ifndef LIBMESH_HAVE_METIS
libmesh_here();
libMesh::err << "ERROR: The library has been built without" << std::endl
<< "Metis support. Using a space-filling curve" << std::endl
<< "partitioner instead!" << std::endl;
SFCPartitioner sfcp;
sfcp.partition (mesh, n_pieces);
// What to do if the Metis library IS present
#else
START_LOG("partition()", "MetisPartitioner");
const dof_id_type n_active_elem = mesh.n_active_elem();
// build the graph
// std::vector<int> options(5);
std::vector<int> vwgt(n_active_elem);
std::vector<int> part(n_active_elem);
int
n = static_cast<int>(n_active_elem), // number of "nodes" (elements)
// in the graph
// wgtflag = 2, // weights on vertices only,
// // none on edges
// numflag = 0, // C-style 0-based numbering
nparts = static_cast<int>(n_pieces), // number of subdomains to create
edgecut = 0; // the numbers of edges cut by the
// resulting partition
// Set the options
// options[0] = 0; // use default options
// Metis will only consider the active elements.
// We need to map the active element ids into a
// contiguous range. Further, we want the unique range indexing to be
// independednt of the element ordering, otherwise a circular dependency
// can result in which the partitioning depends on the ordering which
// depends on the partitioning...
std::map<const Elem*, dof_id_type> global_index_map;
{
std::vector<dof_id_type> global_index;
MeshBase::element_iterator it = mesh.active_elements_begin();
const MeshBase::element_iterator end = mesh.active_elements_end();
MeshCommunication().find_global_indices (MeshTools::bounding_box(mesh),
it, end, global_index);
libmesh_assert_equal_to (global_index.size(), n_active_elem);
for (std::size_t cnt=0; it != end; ++it)
{
const Elem *elem = *it;
libmesh_assert (!global_index_map.count(elem));
global_index_map[elem] = global_index[cnt++];
}
libmesh_assert_equal_to (global_index_map.size(), n_active_elem);
}
// build the graph in CSR format. Note that
// the edges in the graph will correspond to
// face neighbors
std::vector<int> xadj, adjncy;
{
std::vector<const Elem*> neighbors_offspring;
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
// This will be exact when there is no refinement and all the
// elements are of the same type.
std::size_t graph_size=0;
std::vector<std::vector<dof_id_type> > graph(n_active_elem);
for (; elem_it != elem_end; ++elem_it)
{
const Elem* elem = *elem_it;
libmesh_assert (global_index_map.count(elem));
const dof_id_type elem_global_index =
global_index_map[elem];
libmesh_assert_less (elem_global_index, vwgt.size());
libmesh_assert_less (elem_global_index, graph.size());
// maybe there is a better weight?
// The weight is used to define what a balanced graph is
if(!_weights)
vwgt[elem_global_index] = elem->n_nodes();
else
vwgt[elem_global_index] = static_cast<int>((*_weights)[elem->id()]);
// Loop over the element's neighbors. An element
// adjacency corresponds to a face neighbor
for (unsigned int ms=0; ms<elem->n_neighbors(); ms++)
{
const Elem* neighbor = elem->neighbor(ms);
if (neighbor != NULL)
{
// If the neighbor is active treat it
// as a connection
if (neighbor->active())
{
libmesh_assert (global_index_map.count(neighbor));
const dof_id_type neighbor_global_index =
global_index_map[neighbor];
graph[elem_global_index].push_back(neighbor_global_index);
graph_size++;
}
#ifdef LIBMESH_ENABLE_AMR
// Otherwise we need to find all of the
// neighbor's children that are connected to
// us and add them
else
{
// The side of the neighbor to which
// we are connected
const unsigned int ns =
neighbor->which_neighbor_am_i (elem);
libmesh_assert_less (ns, neighbor->n_neighbors());
// Get all the active children (& grandchildren, etc...)
// of the neighbor.
neighbor->active_family_tree (neighbors_offspring);
// Get all the neighbor's children that
// live on that side and are thus connected
// to us
for (unsigned int nc=0; nc<neighbors_offspring.size(); nc++)
{
const Elem* child =
neighbors_offspring[nc];
// This does not assume a level-1 mesh.
// Note that since children have sides numbered
// coincident with the parent then this is a sufficient test.
if (child->neighbor(ns) == elem)
{
libmesh_assert (child->active());
libmesh_assert (global_index_map.count(child));
const dof_id_type child_global_index =
global_index_map[child];
graph[elem_global_index].push_back(child_global_index);
graph_size++;
}
}
}
#endif /* ifdef LIBMESH_ENABLE_AMR */
}
}
}
// Convert the graph into the format Metis wants
xadj.reserve(n_active_elem+1);
adjncy.reserve(graph_size);
for (std::size_t r=0; r<graph.size(); r++)
{
xadj.push_back(adjncy.size());
std::vector<dof_id_type> graph_row; // build this emtpy
graph_row.swap(graph[r]); // this will deallocate at the end of scope
adjncy.insert(adjncy.end(),
graph_row.begin(),
graph_row.end());
}
// The end of the adjacency array for the last elem
xadj.push_back(adjncy.size());
libmesh_assert_equal_to (adjncy.size(), graph_size);
libmesh_assert_equal_to (xadj.size(), n_active_elem+1);
} // done building the graph
if (adjncy.empty())
adjncy.push_back(0);
int ncon = 1;
// Select which type of partitioning to create
// Use recursive if the number of partitions is less than or equal to 8
if (n_pieces <= 8)
Metis::METIS_PartGraphRecursive(&n, &ncon, &xadj[0], &adjncy[0], &vwgt[0], NULL,
NULL, &nparts, NULL, NULL, NULL,
&edgecut, &part[0]);
// Otherwise use kway
else
Metis::METIS_PartGraphKway(&n, &ncon, &xadj[0], &adjncy[0], &vwgt[0], NULL,
NULL, &nparts, NULL, NULL, NULL,
&edgecut, &part[0]);
// Assign the returned processor ids. The part array contains
// the processor id for each active element, but in terms of
// the contiguous indexing we defined above
{
MeshBase::element_iterator it = mesh.active_elements_begin();
const MeshBase::element_iterator end = mesh.active_elements_end();
for (; it!=end; ++it)
{
Elem* elem = *it;
libmesh_assert (global_index_map.count(elem));
const dof_id_type elem_global_index =
global_index_map[elem];
libmesh_assert_less (elem_global_index, part.size());
const processor_id_type elem_procid =
static_cast<processor_id_type>(part[elem_global_index]);
elem->processor_id() = elem_procid;
}
}
STOP_LOG("partition()", "MetisPartitioner");
#endif
}
void
MultiAppUserObjectTransfer::execute()
{
_console << "Beginning MultiAppUserObjectTransfer " << name() << std::endl;
switch (_direction)
{
case TO_MULTIAPP:
{
for (unsigned int i=0; i<_multi_app->numGlobalApps(); i++)
{
if (_multi_app->hasLocalApp(i))
{
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
// Loop over the master nodes and set the value of the variable
System * to_sys = find_sys(_multi_app->appProblem(i)->es(), _to_var_name);
unsigned int sys_num = to_sys->number();
unsigned int var_num = to_sys->variable_number(_to_var_name);
NumericVector<Real> & solution = _multi_app->appTransferVector(i, _to_var_name);
MeshBase * mesh = NULL;
if (_displaced_target_mesh && _multi_app->appProblem(i)->getDisplacedProblem())
{
mesh = &_multi_app->appProblem(i)->getDisplacedProblem()->mesh().getMesh();
}
else
mesh = &_multi_app->appProblem(i)->mesh().getMesh();
bool is_nodal = to_sys->variable_type(var_num).family == LAGRANGE;
const UserObject & user_object = _multi_app->problem()->getUserObjectBase(_user_object_name);
if (is_nodal)
{
MeshBase::const_node_iterator node_it = mesh->local_nodes_begin();
MeshBase::const_node_iterator node_end = mesh->local_nodes_end();
for (; node_it != node_end; ++node_it)
{
Node * node = *node_it;
if (node->n_dofs(sys_num, var_num) > 0) // If this variable has dofs at this node
{
// The zero only works for LAGRANGE!
dof_id_type dof = node->dof_number(sys_num, var_num, 0);
// Swap back
Moose::swapLibMeshComm(swapped);
Real from_value = user_object.spatialValue(*node+_multi_app->position(i));
// Swap again
swapped = Moose::swapLibMeshComm(_multi_app->comm());
solution.set(dof, from_value);
}
}
}
else // Elemental
{
MeshBase::const_element_iterator elem_it = mesh->local_elements_begin();
MeshBase::const_element_iterator elem_end = mesh->local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
Point centroid = elem->centroid();
if (elem->n_dofs(sys_num, var_num) > 0) // If this variable has dofs at this elem
{
// The zero only works for LAGRANGE!
dof_id_type dof = elem->dof_number(sys_num, var_num, 0);
// Swap back
Moose::swapLibMeshComm(swapped);
Real from_value = user_object.spatialValue(centroid+_multi_app->position(i));
// Swap again
swapped = Moose::swapLibMeshComm(_multi_app->comm());
solution.set(dof, from_value);
}
}
}
solution.close();
to_sys->update();
// Swap back
Moose::swapLibMeshComm(swapped);
}
}
break;
}
case FROM_MULTIAPP:
{
FEProblem & to_problem = *_multi_app->problem();
MooseVariable & to_var = to_problem.getVariable(0, _to_var_name);
SystemBase & to_system_base = to_var.sys();
System & to_sys = to_system_base.system();
unsigned int to_sys_num = to_sys.number();
// Only works with a serialized mesh to transfer to!
mooseAssert(to_sys.get_mesh().is_serial(), "MultiAppUserObjectTransfer only works with SerialMesh!");
unsigned int to_var_num = to_sys.variable_number(to_var.name());
_console << "Transferring to: " << to_var.name() << std::endl;
// EquationSystems & to_es = to_sys.get_equation_systems();
//Create a serialized version of the solution vector
NumericVector<Number> * to_solution = to_sys.solution.get();
MeshBase * to_mesh = NULL;
if (_displaced_target_mesh && to_problem.getDisplacedProblem())
to_mesh = &to_problem.getDisplacedProblem()->mesh().getMesh();
else
to_mesh = &to_problem.mesh().getMesh();
bool is_nodal = to_sys.variable_type(to_var_num).family == LAGRANGE;
for (unsigned int i=0; i<_multi_app->numGlobalApps(); i++)
{
if (!_multi_app->hasLocalApp(i))
continue;
Point app_position = _multi_app->position(i);
MeshTools::BoundingBox app_box = _multi_app->getBoundingBox(i);
const UserObject & user_object = _multi_app->appUserObjectBase(i, _user_object_name);
if (is_nodal)
{
MeshBase::const_node_iterator node_it = to_mesh->nodes_begin();
MeshBase::const_node_iterator node_end = to_mesh->nodes_end();
for (; node_it != node_end; ++node_it)
{
Node * node = *node_it;
if (node->n_dofs(to_sys_num, to_var_num) > 0) // If this variable has dofs at this node
{
// See if this node falls in this bounding box
if (app_box.contains_point(*node))
{
dof_id_type dof = node->dof_number(to_sys_num, to_var_num, 0);
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
Real from_value = user_object.spatialValue(*node-app_position);
Moose::swapLibMeshComm(swapped);
to_solution->set(dof, from_value);
}
}
}
}
else // Elemental
{
MeshBase::const_element_iterator elem_it = to_mesh->elements_begin();
MeshBase::const_element_iterator elem_end = to_mesh->elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem * elem = *elem_it;
if (elem->n_dofs(to_sys_num, to_var_num) > 0) // If this variable has dofs at this elem
{
Point centroid = elem->centroid();
// See if this elem falls in this bounding box
if (app_box.contains_point(centroid))
{
dof_id_type dof = elem->dof_number(to_sys_num, to_var_num, 0);
MPI_Comm swapped = Moose::swapLibMeshComm(_multi_app->comm());
Real from_value = user_object.spatialValue(centroid-app_position);
Moose::swapLibMeshComm(swapped);
to_solution->set(dof, from_value);
}
}
}
}
}
to_solution->close();
to_sys.update();
break;
}
}
_console << "Finished MultiAppUserObjectTransfer " << name() << std::endl;
}
void MeshRefinement::flag_elements_by_elem_fraction (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
parallel_object_only();
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// The number of active elements in the mesh
const dof_id_type n_active_elem = _mesh.n_elem();
// The number of elements to flag for coarsening
const dof_id_type n_elem_coarsen =
static_cast<dof_id_type>(_coarsen_fraction * n_active_elem);
// The number of elements to flag for refinement
const dof_id_type n_elem_refine =
static_cast<dof_id_type>(_refine_fraction * n_active_elem);
// Clean up the refinement flags. These could be left
// over from previous refinement steps.
this->clean_refinement_flags();
// This vector stores the error and element number for all the
// active elements. It will be sorted and the top & bottom
// elements will then be flagged for coarsening & refinement
std::vector<ErrorVectorReal> sorted_error;
sorted_error.reserve (n_active_elem);
// Loop over the active elements and create the entry
// in the sorted_error vector
MeshBase::element_iterator elem_it = _mesh.active_local_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_local_elements_end();
for (; elem_it != elem_end; ++elem_it)
sorted_error.push_back (error_per_cell[(*elem_it)->id()]);
this->comm().allgather(sorted_error);
// Now sort the sorted_error vector
std::sort (sorted_error.begin(), sorted_error.end());
// If we're coarsening by parents:
// Create a sorted error vector with coarsenable parent elements
// only, sorted by lowest errors first
ErrorVector error_per_parent, sorted_parent_error;
if (_coarsen_by_parents)
{
Real parent_error_min, parent_error_max;
create_parent_error_vector(error_per_cell,
error_per_parent,
parent_error_min,
parent_error_max);
sorted_parent_error = error_per_parent;
std::sort (sorted_parent_error.begin(), sorted_parent_error.end());
// All the other error values will be 0., so get rid of them.
sorted_parent_error.erase (std::remove(sorted_parent_error.begin(),
sorted_parent_error.end(), 0.),
sorted_parent_error.end());
}
ErrorVectorReal top_error= 0., bottom_error = 0.;
// Get the maximum error value corresponding to the
// bottom n_elem_coarsen elements
if (_coarsen_by_parents && n_elem_coarsen)
{
const unsigned int dim = _mesh.mesh_dimension();
unsigned int twotodim = 1;
for (unsigned int i=0; i!=dim; ++i)
twotodim *= 2;
dof_id_type n_parent_coarsen = n_elem_coarsen / (twotodim - 1);
if (n_parent_coarsen)
bottom_error = sorted_parent_error[n_parent_coarsen - 1];
}
else if (n_elem_coarsen)
{
bottom_error = sorted_error[n_elem_coarsen - 1];
}
if (n_elem_refine)
top_error = sorted_error[sorted_error.size() - n_elem_refine];
// Finally, let's do the element flagging
elem_it = _mesh.active_elements_begin();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
Elem* parent = elem->parent();
if (_coarsen_by_parents && parent && n_elem_coarsen &&
error_per_parent[parent->id()] <= bottom_error)
elem->set_refinement_flag(Elem::COARSEN);
if (!_coarsen_by_parents && n_elem_coarsen &&
error_per_cell[elem->id()] <= bottom_error)
elem->set_refinement_flag(Elem::COARSEN);
if (n_elem_refine &&
elem->level() < _max_h_level &&
error_per_cell[elem->id()] >= top_error)
elem->set_refinement_flag(Elem::REFINE);
}
}
void MeshRefinement::flag_elements_by_mean_stddev (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// Get the mean value from the error vector
const Real mean = error_per_cell.mean();
// Get the standard deviation. This equals the
// square-root of the variance
const Real stddev = std::sqrt (error_per_cell.variance());
// Check for valid fractions
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// The refine and coarsen cutoff
const Real refine_cutoff = mean + _refine_fraction * stddev;
const Real coarsen_cutoff = std::max(mean - _coarsen_fraction * stddev, 0.);
// Loop over the elements and flag them for coarsening or
// refinement based on the element error
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
const dof_id_type id = elem->id();
libmesh_assert_less (id, error_per_cell.size());
const ErrorVectorReal elem_error = error_per_cell[id];
// Possibly flag the element for coarsening ...
if (elem_error <= coarsen_cutoff)
elem->set_refinement_flag(Elem::COARSEN);
// ... or refinement
if ((elem_error >= refine_cutoff) && (elem->level() < _max_h_level))
elem->set_refinement_flag(Elem::REFINE);
}
}
bool MeshRefinement::flag_elements_by_nelem_target (const ErrorVector& error_per_cell)
{
parallel_object_only();
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// This function is currently only coded to work when coarsening by
// parents - it's too hard to guess how many coarsenings will be
// performed otherwise.
libmesh_assert (_coarsen_by_parents);
// The number of active elements in the mesh - hopefully less than
// 2 billion on 32 bit machines
const dof_id_type n_active_elem = _mesh.n_active_elem();
// The maximum number of active elements to flag for coarsening
const dof_id_type max_elem_coarsen =
static_cast<dof_id_type>(_coarsen_fraction * n_active_elem) + 1;
// The maximum number of elements to flag for refinement
const dof_id_type max_elem_refine =
static_cast<dof_id_type>(_refine_fraction * n_active_elem) + 1;
// Clean up the refinement flags. These could be left
// over from previous refinement steps.
this->clean_refinement_flags();
// The target number of elements to add or remove
const std::ptrdiff_t n_elem_new = _nelem_target - n_active_elem;
// Create an vector with active element errors and ids,
// sorted by highest errors first
const dof_id_type max_elem_id = _mesh.max_elem_id();
std::vector<std::pair<ErrorVectorReal, dof_id_type> > sorted_error;
sorted_error.reserve (n_active_elem);
// On a ParallelMesh, we need to communicate to know which remote ids
// correspond to active elements.
{
std::vector<bool> is_active(max_elem_id, false);
MeshBase::element_iterator elem_it = _mesh.active_local_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const dof_id_type eid = (*elem_it)->id();
is_active[eid] = true;
libmesh_assert_less (eid, error_per_cell.size());
sorted_error.push_back
(std::make_pair(error_per_cell[eid], eid));
}
this->comm().max(is_active);
this->comm().allgather(sorted_error);
}
// Default sort works since pairs are sorted lexicographically
std::sort (sorted_error.begin(), sorted_error.end());
std::reverse (sorted_error.begin(), sorted_error.end());
// Create a sorted error vector with coarsenable parent elements
// only, sorted by lowest errors first
ErrorVector error_per_parent;
std::vector<std::pair<ErrorVectorReal, dof_id_type> > sorted_parent_error;
Real parent_error_min, parent_error_max;
create_parent_error_vector(error_per_cell,
error_per_parent,
parent_error_min,
parent_error_max);
// create_parent_error_vector sets values for non-parents and
// non-coarsenable parents to -1. Get rid of them.
for (dof_id_type i=0; i != error_per_parent.size(); ++i)
if (error_per_parent[i] != -1)
sorted_parent_error.push_back(std::make_pair(error_per_parent[i], i));
std::sort (sorted_parent_error.begin(), sorted_parent_error.end());
// Keep track of how many elements we plan to coarsen & refine
dof_id_type coarsen_count = 0;
dof_id_type refine_count = 0;
const unsigned int dim = _mesh.mesh_dimension();
unsigned int twotodim = 1;
for (unsigned int i=0; i!=dim; ++i)
twotodim *= 2;
// First, let's try to get our element count to target_nelem
if (n_elem_new >= 0)
{
// Every element refinement creates at least
// 2^dim-1 new elements
refine_count =
std::min(libmesh_cast_int<dof_id_type>(n_elem_new / (twotodim-1)),
max_elem_refine);
}
else
{
// Every successful element coarsening is likely to destroy
// 2^dim-1 net elements.
coarsen_count =
std::min(libmesh_cast_int<dof_id_type>(-n_elem_new / (twotodim-1)),
max_elem_coarsen);
}
// Next, let's see if we can trade any refinement for coarsening
while (coarsen_count < max_elem_coarsen &&
refine_count < max_elem_refine &&
coarsen_count < sorted_parent_error.size() &&
refine_count < sorted_error.size() &&
sorted_error[refine_count].first >
sorted_parent_error[coarsen_count].first * _coarsen_threshold)
{
coarsen_count++;
refine_count++;
}
// On a ParallelMesh, we need to communicate to know which remote ids
// correspond to refinable elements
dof_id_type successful_refine_count = 0;
{
std::vector<bool> is_refinable(max_elem_id, false);
for (dof_id_type i=0; i != sorted_error.size(); ++i)
{
dof_id_type eid = sorted_error[i].second;
Elem *elem = _mesh.query_elem(eid);
if (elem && elem->level() < _max_h_level)
is_refinable[eid] = true;
}
this->comm().max(is_refinable);
if (refine_count > max_elem_refine)
refine_count = max_elem_refine;
for (dof_id_type i=0; i != sorted_error.size(); ++i)
{
if (successful_refine_count >= refine_count)
break;
dof_id_type eid = sorted_error[i].second;
Elem *elem = _mesh.query_elem(eid);
if (is_refinable[eid])
{
if (elem)
elem->set_refinement_flag(Elem::REFINE);
successful_refine_count++;
}
}
}
// If we couldn't refine enough elements, don't coarsen too many
// either
if (coarsen_count < (refine_count - successful_refine_count))
coarsen_count = 0;
else
coarsen_count -= (refine_count - successful_refine_count);
if (coarsen_count > max_elem_coarsen)
coarsen_count = max_elem_coarsen;
dof_id_type successful_coarsen_count = 0;
if (coarsen_count)
{
for (dof_id_type i=0; i != sorted_parent_error.size(); ++i)
{
if (successful_coarsen_count >= coarsen_count * twotodim)
break;
dof_id_type parent_id = sorted_parent_error[i].second;
Elem *parent = _mesh.query_elem(parent_id);
// On a ParallelMesh we skip remote elements
if (!parent)
continue;
libmesh_assert(parent->has_children());
for (unsigned int c=0; c != parent->n_children(); ++c)
{
Elem *elem = parent->child(c);
if (elem && elem != remote_elem)
{
libmesh_assert(elem->active());
elem->set_refinement_flag(Elem::COARSEN);
successful_coarsen_count++;
}
}
}
}
// Return true if we've done all the AMR/C we can
if (!successful_coarsen_count &&
!successful_refine_count)
return true;
// And false if there may still be more to do.
return false;
}
//-----------------------------------------------------------------
// Mesh refinement methods
void MeshRefinement::flag_elements_by_error_fraction (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
parallel_object_only();
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// Clean up the refinement flags. These could be left
// over from previous refinement steps.
this->clean_refinement_flags();
// We're getting the minimum and maximum error values
// for the ACTIVE elements
Real error_min = 1.e30;
Real error_max = 0.;
// And, if necessary, for their parents
Real parent_error_min = 1.e30;
Real parent_error_max = 0.;
// Prepare another error vector if we need to sum parent errors
ErrorVector error_per_parent;
if (_coarsen_by_parents)
{
create_parent_error_vector(error_per_cell,
error_per_parent,
parent_error_min,
parent_error_max);
}
// We need to loop over all active elements to find the minimum
MeshBase::element_iterator el_it =
_mesh.active_local_elements_begin();
const MeshBase::element_iterator el_end =
_mesh.active_local_elements_end();
for (; el_it != el_end; ++el_it)
{
const dof_id_type id = (*el_it)->id();
libmesh_assert_less (id, error_per_cell.size());
error_max = std::max (error_max, error_per_cell[id]);
error_min = std::min (error_min, error_per_cell[id]);
}
this->comm().max(error_max);
this->comm().min(error_min);
// Compute the cutoff values for coarsening and refinement
const Real error_delta = (error_max - error_min);
const Real parent_error_delta = parent_error_max - parent_error_min;
const Real refine_cutoff = (1.- _refine_fraction)*error_max;
const Real coarsen_cutoff = _coarsen_fraction*error_delta + error_min;
const Real parent_cutoff = _coarsen_fraction*parent_error_delta + error_min;
// // Print information about the error
// libMesh::out << " Error Information:" << std::endl
// << " ------------------" << std::endl
// << " min: " << error_min << std::endl
// << " max: " << error_max << std::endl
// << " delta: " << error_delta << std::endl
// << " refine_cutoff: " << refine_cutoff << std::endl
// << " coarsen_cutoff: " << coarsen_cutoff << std::endl;
// Loop over the elements and flag them for coarsening or
// refinement based on the element error
MeshBase::element_iterator e_it =
_mesh.active_elements_begin();
const MeshBase::element_iterator e_end =
_mesh.active_elements_end();
for (; e_it != e_end; ++e_it)
{
Elem* elem = *e_it;
const dof_id_type id = elem->id();
libmesh_assert_less (id, error_per_cell.size());
const ErrorVectorReal elem_error = error_per_cell[id];
if (_coarsen_by_parents)
{
Elem* parent = elem->parent();
if (parent)
{
const dof_id_type parentid = parent->id();
if (error_per_parent[parentid] >= 0. &&
error_per_parent[parentid] <= parent_cutoff)
elem->set_refinement_flag(Elem::COARSEN);
}
}
// Flag the element for coarsening if its error
// is <= coarsen_fraction*delta + error_min
else if (elem_error <= coarsen_cutoff)
{
elem->set_refinement_flag(Elem::COARSEN);
}
// Flag the element for refinement if its error
// is >= refinement_cutoff.
if (elem_error >= refine_cutoff)
if (elem->level() < _max_h_level)
elem->set_refinement_flag(Elem::REFINE);
}
}
void MeshRefinement::flag_elements_by_error_tolerance (const ErrorVector& error_per_cell_in)
{
parallel_object_only();
libmesh_assert_greater (_coarsen_threshold, 0);
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// How much error per cell will we tolerate?
const Real local_refinement_tolerance =
_absolute_global_tolerance / std::sqrt(static_cast<Real>(_mesh.n_active_elem()));
const Real local_coarsening_tolerance =
local_refinement_tolerance * _coarsen_threshold;
// Prepare another error vector if we need to sum parent errors
ErrorVector error_per_parent;
if (_coarsen_by_parents)
{
Real parent_error_min, parent_error_max;
create_parent_error_vector(error_per_cell_in,
error_per_parent,
parent_error_min,
parent_error_max);
}
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
Elem* parent = elem->parent();
const dof_id_type elem_number = elem->id();
const ErrorVectorReal elem_error = error_per_cell_in[elem_number];
if (elem_error > local_refinement_tolerance &&
elem->level() < _max_h_level)
elem->set_refinement_flag(Elem::REFINE);
if (!_coarsen_by_parents && elem_error <
local_coarsening_tolerance)
elem->set_refinement_flag(Elem::COARSEN);
if (_coarsen_by_parents && parent)
{
ErrorVectorReal parent_error = error_per_parent[parent->id()];
if (parent_error >= 0.)
{
const Real parent_coarsening_tolerance =
std::sqrt(parent->n_children() *
local_coarsening_tolerance *
local_coarsening_tolerance);
if (parent_error < parent_coarsening_tolerance)
elem->set_refinement_flag(Elem::COARSEN);
}
}
}
}
void ExodusII_IO::read (const std::string & fname)
{
// Get a reference to the mesh we are reading
MeshBase & mesh = MeshInput<MeshBase>::mesh();
// Clear any existing mesh data
mesh.clear();
// Keep track of what kinds of elements this file contains
elems_of_dimension.clear();
elems_of_dimension.resize(4, false);
#ifdef DEBUG
this->verbose(true);
#endif
// Instantiate the ElementMaps interface
ExodusII_IO_Helper::ElementMaps em(*exio_helper);
// Open the exodus file in EX_READ mode
exio_helper->open(fname.c_str(), /*read_only=*/true);
// Get header information from exodus file
exio_helper->read_header();
// Read the QA records
exio_helper->read_qa_records();
// Print header information
exio_helper->print_header();
// Read nodes from the exodus file
exio_helper->read_nodes();
// Reserve space for the nodes.
mesh.reserve_nodes(exio_helper->num_nodes);
// Read the node number map from the Exodus file. This is
// required if we want to preserve the numbering of nodes as it
// exists in the Exodus file. If the Exodus file does not contain
// a node_num_map, the identity map is returned by this call.
exio_helper->read_node_num_map();
// Loop over the nodes, create Nodes with local processor_id 0.
for (int i=0; i<exio_helper->num_nodes; i++)
{
// Use the node_num_map to get the correct ID for Exodus
int exodus_id = exio_helper->node_num_map[i];
// Catch the node that was added to the mesh
Node * added_node = mesh.add_point (Point(exio_helper->x[i], exio_helper->y[i], exio_helper->z[i]), exodus_id-1);
// If the Mesh assigned an ID different from what is in the
// Exodus file, we should probably error.
if (added_node->id() != static_cast<unsigned>(exodus_id-1))
libmesh_error_msg("Error! Mesh assigned node ID " \
<< added_node->id() \
<< " which is different from the (zero-based) Exodus ID " \
<< exodus_id-1 \
<< "!");
}
// This assert is no longer valid if the nodes are not numbered
// sequentially starting from 1 in the Exodus file.
// libmesh_assert_equal_to (static_cast<unsigned int>(exio_helper->num_nodes), mesh.n_nodes());
// Get information about all the blocks
exio_helper->read_block_info();
// Reserve space for the elements
mesh.reserve_elem(exio_helper->num_elem);
// Read the element number map from the Exodus file. This is
// required if we want to preserve the numbering of elements as it
// exists in the Exodus file. If the Exodus file does not contain
// an elem_num_map, the identity map is returned by this call.
exio_helper->read_elem_num_map();
// Read in the element connectivity for each block.
int nelem_last_block = 0;
// Loop over all the blocks
for (int i=0; i<exio_helper->num_elem_blk; i++)
{
// Read the information for block i
exio_helper->read_elem_in_block (i);
int subdomain_id = exio_helper->get_block_id(i);
// populate the map of names
std::string subdomain_name = exio_helper->get_block_name(i);
if (!subdomain_name.empty())
mesh.subdomain_name(static_cast<subdomain_id_type>(subdomain_id)) = subdomain_name;
// Set any relevant node/edge maps for this element
const std::string type_str (exio_helper->get_elem_type());
const ExodusII_IO_Helper::Conversion conv = em.assign_conversion(type_str);
// Loop over all the faces in this block
int jmax = nelem_last_block+exio_helper->num_elem_this_blk;
for (int j=nelem_last_block; j<jmax; j++)
{
Elem * elem = Elem::build (conv.get_canonical_type()).release();
libmesh_assert (elem);
elem->subdomain_id() = static_cast<subdomain_id_type>(subdomain_id) ;
// Use the elem_num_map to obtain the ID of this element in the Exodus file
int exodus_id = exio_helper->elem_num_map[j];
// Assign this element the same ID it had in the Exodus
// file, but make it zero-based by subtracting 1. Note:
// some day we could use 1-based numbering in libmesh and
// thus match the Exodus numbering exactly, but at the
// moment libmesh is zero-based.
elem->set_id(exodus_id-1);
// Record that we have seen an element of dimension elem->dim()
elems_of_dimension[elem->dim()] = true;
// Catch the Elem pointer that the Mesh throws back
elem = mesh.add_elem (elem);
// If the Mesh assigned an ID different from what is in the
// Exodus file, we should probably error.
if (elem->id() != static_cast<unsigned>(exodus_id-1))
libmesh_error_msg("Error! Mesh assigned ID " \
<< elem->id() \
<< " which is different from the (zero-based) Exodus ID " \
<< exodus_id-1 \
<< "!");
// Set all the nodes for this element
for (int k=0; k<exio_helper->num_nodes_per_elem; k++)
{
// global index
int gi = (j-nelem_last_block)*exio_helper->num_nodes_per_elem + conv.get_node_map(k);
// The entries in 'connect' are actually (1-based)
// indices into the node_num_map, so to get the right
// node ID we:
// 1.) Subtract 1 from connect[gi]
// 2.) Pass it through node_num_map to get the corresponding Exodus ID
// 3.) Subtract 1 from that, since libmesh node numbering is "zero"-based,
// even when the Exodus node numbering doesn't start with 1.
int libmesh_node_id = exio_helper->node_num_map[exio_helper->connect[gi] - 1] - 1;
// Set the node pointer in the Elem
elem->set_node(k) = mesh.node_ptr(libmesh_node_id);
}
}
// running sum of # of elements per block,
// (should equal total number of elements in the end)
nelem_last_block += exio_helper->num_elem_this_blk;
}
// This assert isn't valid if the Exodus file's numbering doesn't
// start with 1! For example, if Exodus's elem_num_map is 21, 22,
// 23, 24, 25, 26, 27, 28, 29, 30, ... 84, then by the time you are
// done with the loop above, mesh.n_elem() will report 84 and
// nelem_last_block will be 64.
// libmesh_assert_equal_to (static_cast<unsigned>(nelem_last_block), mesh.n_elem());
// Set the mesh dimension to the largest encountered for an element
for (unsigned char i=0; i!=4; ++i)
if (elems_of_dimension[i])
mesh.set_mesh_dimension(i);
// Read in sideset information -- this is useful for applying boundary conditions
{
// Get basic information about all sidesets
exio_helper->read_sideset_info();
int offset=0;
for (int i=0; i<exio_helper->num_side_sets; i++)
{
// Compute new offset
offset += (i > 0 ? exio_helper->num_sides_per_set[i-1] : 0);
exio_helper->read_sideset (i, offset);
std::string sideset_name = exio_helper->get_side_set_name(i);
if (!sideset_name.empty())
mesh.get_boundary_info().sideset_name
(cast_int<boundary_id_type>(exio_helper->get_side_set_id(i)))
= sideset_name;
}
for (unsigned int e=0; e<exio_helper->elem_list.size(); e++)
{
// The numbers in the Exodus file sidesets should be thought
// of as (1-based) indices into the elem_num_map array. So,
// to get the right element ID we have to:
// 1.) Subtract 1 from elem_list[e] (to get a zero-based index)
// 2.) Pass it through elem_num_map (to get the corresponding Exodus ID)
// 3.) Subtract 1 from that, since libmesh is "zero"-based,
// even when the Exodus numbering doesn't start with 1.
dof_id_type libmesh_elem_id =
cast_int<dof_id_type>(exio_helper->elem_num_map[exio_helper->elem_list[e] - 1] - 1);
// Set any relevant node/edge maps for this element
Elem * elem = mesh.elem(libmesh_elem_id);
const ExodusII_IO_Helper::Conversion conv = em.assign_conversion(elem->type());
// Map the zero-based Exodus side numbering to the libmesh side numbering
int mapped_side = conv.get_side_map(exio_helper->side_list[e]-1);
// Check for errors
if (mapped_side == ExodusII_IO_Helper::Conversion::invalid_id)
libmesh_error_msg("Invalid 1-based side id: " \
<< exio_helper->side_list[e] \
<< " detected for " \
<< Utility::enum_to_string(elem->type()));
// Add this (elem,side,id) triplet to the BoundaryInfo object.
mesh.get_boundary_info().add_side (libmesh_elem_id,
cast_int<unsigned short>(mapped_side),
cast_int<boundary_id_type>(exio_helper->id_list[e]));
}
}
// Read nodeset info
{
exio_helper->read_nodeset_info();
for (int nodeset=0; nodeset<exio_helper->num_node_sets; nodeset++)
{
boundary_id_type nodeset_id =
cast_int<boundary_id_type>(exio_helper->nodeset_ids[nodeset]);
std::string nodeset_name = exio_helper->get_node_set_name(nodeset);
if (!nodeset_name.empty())
mesh.get_boundary_info().nodeset_name(nodeset_id) = nodeset_name;
exio_helper->read_nodeset(nodeset);
for (unsigned int node=0; node<exio_helper->node_list.size(); node++)
{
// As before, the entries in 'node_list' are 1-based
// indcies into the node_num_map array, so we have to map
// them. See comment above.
int libmesh_node_id = exio_helper->node_num_map[exio_helper->node_list[node] - 1] - 1;
mesh.get_boundary_info().add_node(cast_int<dof_id_type>(libmesh_node_id),
nodeset_id);
}
}
}
#if LIBMESH_DIM < 3
if (mesh.mesh_dimension() > LIBMESH_DIM)
libmesh_error_msg("Cannot open dimension " \
<< mesh.mesh_dimension() \
<< " mesh file when configured without " \
<< mesh.mesh_dimension() \
<< "D support.");
#endif
}
// ------------------------------------------------------------
// SFCPartitioner implementation
void SFCPartitioner::_do_partition (MeshBase& mesh,
const unsigned int n)
{
libmesh_assert_greater (n, 0);
// Check for an easy return
if (n == 1)
{
this->single_partition (mesh);
return;
}
// What to do if the sfcurves library IS NOT present
#ifndef LIBMESH_HAVE_SFCURVES
libmesh_here();
libMesh::err << "ERROR: The library has been built without" << std::endl
<< "Space Filling Curve support. Using a linear" << std::endl
<< "partitioner instead!" << std::endl;
LinearPartitioner lp;
lp.partition (mesh, n);
// What to do if the sfcurves library IS present
#else
START_LOG("sfc_partition()", "SFCPartitioner");
const unsigned int n_active_elem = mesh.n_active_elem();
const unsigned int n_elem = mesh.n_elem();
// the forward_map maps the active element id
// into a contiguous block of indices
std::vector<unsigned int>
forward_map (n_elem, libMesh::invalid_uint);
// the reverse_map maps the contiguous ids back
// to active elements
std::vector<Elem*> reverse_map (n_active_elem, NULL);
int size = static_cast<int>(n_active_elem);
std::vector<double> x (size);
std::vector<double> y (size);
std::vector<double> z (size);
std::vector<int> table (size);
// We need to map the active element ids into a
// contiguous range.
{
// active_elem_iterator elem_it (mesh.elements_begin());
// const active_elem_iterator elem_end(mesh.elements_end());
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
unsigned int el_num = 0;
for (; elem_it != elem_end; ++elem_it)
{
libmesh_assert_less ((*elem_it)->id(), forward_map.size());
libmesh_assert_less (el_num, reverse_map.size());
forward_map[(*elem_it)->id()] = el_num;
reverse_map[el_num] = *elem_it;
el_num++;
}
libmesh_assert_equal_to (el_num, n_active_elem);
}
// Get the centroid for each active element
{
// const_active_elem_iterator elem_it (mesh.const_elements_begin());
// const const_active_elem_iterator elem_end(mesh.const_elements_end());
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem* elem = *elem_it;
libmesh_assert_less (elem->id(), forward_map.size());
const Point p = elem->centroid();
x[forward_map[elem->id()]] = p(0);
y[forward_map[elem->id()]] = p(1);
z[forward_map[elem->id()]] = p(2);
}
}
// build the space-filling curve
if (_sfc_type == "Hilbert")
Sfc::hilbert (&x[0], &y[0], &z[0], &size, &table[0]);
else if (_sfc_type == "Morton")
Sfc::morton (&x[0], &y[0], &z[0], &size, &table[0]);
else
{
libmesh_here();
libMesh::err << "ERROR: Unknown type: " << _sfc_type << std::endl
<< " Valid types are" << std::endl
<< " \"Hilbert\"" << std::endl
<< " \"Morton\"" << std::endl
<< " " << std::endl
<< "Proceeding with a Hilbert curve." << std::endl;
Sfc::hilbert (&x[0], &y[0], &z[0], &size, &table[0]);
}
// Assign the partitioning to the active elements
{
// {
// std::ofstream out ("sfc.dat");
// out << "variables=x,y,z" << std::endl;
// out << "zone f=point" << std::endl;
// for (unsigned int i=0; i<n_active_elem; i++)
// out << x[i] << " "
// << y[i] << " "
// << z[i] << std::endl;
// }
const unsigned int blksize = (n_active_elem+n-1)/n;
for (unsigned int i=0; i<n_active_elem; i++)
{
libmesh_assert_less (static_cast<unsigned int>(table[i]-1), reverse_map.size());
Elem* elem = reverse_map[table[i]-1];
elem->processor_id() = i/blksize;
}
}
STOP_LOG("sfc_partition()", "SFCPartitioner");
#endif
}
void ParmetisPartitioner::assign_partitioning (MeshBase& mesh)
{
// This function must be run on all processors at once
libmesh_parallel_only(mesh.comm());
const dof_id_type
first_local_elem = _vtxdist[mesh.processor_id()];
std::vector<std::vector<dof_id_type> >
requested_ids(mesh.n_processors()),
requests_to_fill(mesh.n_processors());
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
MeshBase::element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem *elem = *elem_it;
// we need to get the index from the owning processor
// (note we cannot assign it now -- we are iterating
// over elements again and this will be bad!)
libmesh_assert_less (elem->processor_id(), requested_ids.size());
requested_ids[elem->processor_id()].push_back(elem->id());
}
// Trade with all processors (including self) to get their indices
for (processor_id_type pid=0; pid<mesh.n_processors(); pid++)
{
// Trade my requests with processor procup and procdown
const processor_id_type procup = (mesh.processor_id() + pid) %
mesh.n_processors();
const processor_id_type procdown = (mesh.n_processors() +
mesh.processor_id() - pid) %
mesh.n_processors();
mesh.comm().send_receive (procup, requested_ids[procup],
procdown, requests_to_fill[procdown]);
// we can overwrite these requested ids in-place.
for (std::size_t i=0; i<requests_to_fill[procdown].size(); i++)
{
const dof_id_type requested_elem_index =
requests_to_fill[procdown][i];
libmesh_assert(_global_index_by_pid_map.count(requested_elem_index));
const dof_id_type global_index_by_pid =
_global_index_by_pid_map[requested_elem_index];
const dof_id_type local_index =
global_index_by_pid - first_local_elem;
libmesh_assert_less (local_index, _part.size());
libmesh_assert_less (local_index, mesh.n_active_local_elem());
const unsigned int elem_procid =
static_cast<unsigned int>(_part[local_index]);
libmesh_assert_less (elem_procid, static_cast<unsigned int>(_nparts));
requests_to_fill[procdown][i] = elem_procid;
}
// Trade back
mesh.comm().send_receive (procdown, requests_to_fill[procdown],
procup, requested_ids[procup]);
}
// and finally assign the partitioning.
// note we are iterating in exactly the same order
// used to build up the request, so we can expect the
// required entries to be in the proper sequence.
elem_it = mesh.active_elements_begin();
elem_end = mesh.active_elements_end();
for (std::vector<unsigned int> counters(mesh.n_processors(), 0);
elem_it != elem_end; ++elem_it)
{
Elem *elem = *elem_it;
const processor_id_type current_pid = elem->processor_id();
libmesh_assert_less (counters[current_pid], requested_ids[current_pid].size());
const processor_id_type elem_procid =
requested_ids[current_pid][counters[current_pid]++];
libmesh_assert_less (elem_procid, static_cast<unsigned int>(_nparts));
elem->processor_id() = elem_procid;
}
}
// Begin the main program.
int main (int argc, char ** argv)
{
// Initialize libMesh and any dependent libaries, like in example 2.
LibMeshInit init (argc, argv);
// Declare a performance log for the main program
// PerfLog perf_main("Main Program");
// Create a GetPot object to parse the command line
GetPot command_line (argc, argv);
// Check for proper calling arguments.
if (argc < 3)
{
// This handy function will print the file name, line number,
// specified message, and then throw an exception.
libmesh_error_msg("Usage:\n" << "\t " << argv[0] << " -d 2(3)" << " -n 15");
}
// Brief message to the user regarding the program name
// and command line arguments.
else
{
libMesh::out << "Running " << argv[0];
for (int i=1; i<argc; i++)
libMesh::out << " " << argv[i];
libMesh::out << std::endl << std::endl;
}
// Read problem dimension from command line. Use int
// instead of unsigned since the GetPot overload is ambiguous
// otherwise.
int dim = 2;
if (command_line.search(1, "-d"))
dim = command_line.next(dim);
// Skip higher-dimensional examples on a lower-dimensional libMesh build
libmesh_example_requires(dim <= LIBMESH_DIM, "2D/3D support");
// Create a mesh with user-defined dimension on the default MPI
// communicator.
Mesh mesh (init.comm(), dim);
// Read number of elements from command line
int ps = 15;
if (command_line.search(1, "-n"))
ps = command_line.next(ps);
// Read FE order from command line
std::string order = "SECOND";
if (command_line.search(2, "-Order", "-o"))
order = command_line.next(order);
// Read FE Family from command line
std::string family = "LAGRANGE";
if (command_line.search(2, "-FEFamily", "-f"))
family = command_line.next(family);
// Cannot use discontinuous basis.
if ((family == "MONOMIAL") || (family == "XYZ"))
{
if (mesh.processor_id() == 0)
libmesh_error_msg("This example requires a C^0 (or higher) FE basis.");
}
// Use the MeshTools::Generation mesh generator to create a uniform
// grid on the square [-1,1]^D. We instruct the mesh generator
// to build a mesh of 8x8 Quad9 elements in 2D, or Hex27
// elements in 3D. Building these higher-order elements allows
// us to use higher-order approximation, as in example 3.
Real halfwidth = dim > 1 ? 1. : 0.;
Real halfheight = dim > 2 ? 1. : 0.;
if ((family == "LAGRANGE") && (order == "FIRST"))
{
// No reason to use high-order geometric elements if we are
// solving with low-order finite elements.
MeshTools::Generation::build_cube (mesh,
ps,
(dim>1) ? ps : 0,
(dim>2) ? ps : 0,
-1., 1.,
-halfwidth, halfwidth,
-halfheight, halfheight,
(dim==1) ? EDGE2 :
((dim == 2) ? QUAD4 : HEX8));
}
else
{
MeshTools::Generation::build_cube (mesh,
ps,
(dim>1) ? ps : 0,
(dim>2) ? ps : 0,
-1., 1.,
-halfwidth, halfwidth,
-halfheight, halfheight,
(dim==1) ? EDGE3 :
((dim == 2) ? QUAD9 : HEX27));
}
{
MeshBase::element_iterator el = mesh.elements_begin();
const MeshBase::element_iterator end_el = mesh.elements_end();
for ( ; el != end_el; ++el)
{
Elem * elem = *el;
const Point cent = elem->centroid();
if (dim > 1)
{
if ((cent(0) > 0) == (cent(1) > 0))
elem->subdomain_id() = 1;
}
else
{
if (cent(0) > 0)
elem->subdomain_id() = 1;
}
}
}
// Print information about the mesh to the screen.
mesh.print_info();
// Create an equation systems object.
EquationSystems equation_systems (mesh);
// Declare the system and its variables.
// Create a system named "Poisson"
LinearImplicitSystem & system =
equation_systems.add_system<LinearImplicitSystem> ("Poisson");
std::set<subdomain_id_type> active_subdomains;
// Add the variable "u" to "Poisson". "u"
// will be approximated using second-order approximation.
active_subdomains.clear(); active_subdomains.insert(0);
system.add_variable("u",
Utility::string_to_enum<Order> (order),
Utility::string_to_enum<FEFamily>(family),
&active_subdomains);
// Add the variable "v" to "Poisson". "v"
// will be approximated using second-order approximation.
active_subdomains.clear(); active_subdomains.insert(1);
system.add_variable("v",
Utility::string_to_enum<Order> (order),
Utility::string_to_enum<FEFamily>(family),
&active_subdomains);
// Give the system a pointer to the matrix assembly
// function.
system.attach_assemble_function (assemble_poisson);
// Initialize the data structures for the equation system.
equation_systems.init();
// Print information about the system to the screen.
equation_systems.print_info();
mesh.print_info();
// Solve the system "Poisson", just like example 2.
equation_systems.get_system("Poisson").solve();
// After solving the system write the solution
// to a GMV-formatted plot file.
if (dim == 1)
{
GnuPlotIO plot(mesh, "Subdomains Example 2, 1D", GnuPlotIO::GRID_ON);
plot.write_equation_systems("gnuplot_script", equation_systems);
}
else
{
#ifdef LIBMESH_HAVE_EXODUS_API
ExodusII_IO (mesh).write_equation_systems ((dim == 3) ?
"out_3.e" : "out_2.e", equation_systems);
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
}
// All done.
return 0;
}
void
FeatureFloodCount::FeatureData::updateBBoxExtremes(MeshTools::BoundingBox & bbox, const Elem & elem)
{
for (auto node_n = decltype(elem.n_nodes())(0); node_n < elem.n_nodes(); ++node_n)
updateBBoxExtremes(bbox, *(elem.get_node(node_n)));
}
int main(int argc, char** argv)
{
LibMeshInit init(argc, argv);
GetPot cl(argc, argv);
int dim = -1;
if (!cl.search("--dim"))
{
std::cerr << "No --dim argument found!" << std::endl;
usage_error(argv[0]);
}
dim = cl.next(dim);
Mesh mesh(dim);
if(!cl.search("--input"))
{
std::cerr << "No --input argument found!" << std::endl;
usage_error(argv[0]);
}
const char* meshname = cl.next("mesh.xda");
mesh.read(meshname);
std::cout << "Loaded mesh " << meshname << std::endl;
if(!cl.search("--newbcid"))
{
std::cerr << "No --bcid argument found!" << std::endl;
usage_error(argv[0]);
}
boundary_id_type bcid = 0;
bcid = cl.next(bcid);
Point minnormal(-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max());
Point maxnormal(std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max());
Point minpoint(-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max(),
-std::numeric_limits<Real>::max());
Point maxpoint(std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max(),
std::numeric_limits<Real>::max());
if (cl.search("--minnormalx"))
minnormal(0) = cl.next(minnormal(0));
if (cl.search("--minnormalx"))
minnormal(0) = cl.next(minnormal(0));
if (cl.search("--maxnormalx"))
maxnormal(0) = cl.next(maxnormal(0));
if (cl.search("--minnormaly"))
minnormal(1) = cl.next(minnormal(1));
if (cl.search("--maxnormaly"))
maxnormal(1) = cl.next(maxnormal(1));
if (cl.search("--minnormalz"))
minnormal(2) = cl.next(minnormal(2));
if (cl.search("--maxnormalz"))
maxnormal(2) = cl.next(maxnormal(2));
if (cl.search("--minpointx"))
minpoint(0) = cl.next(minpoint(0));
if (cl.search("--maxpointx"))
maxpoint(0) = cl.next(maxpoint(0));
if (cl.search("--minpointy"))
minpoint(1) = cl.next(minpoint(1));
if (cl.search("--maxpointy"))
maxpoint(1) = cl.next(maxpoint(1));
if (cl.search("--minpointz"))
minpoint(2) = cl.next(minpoint(2));
if (cl.search("--maxpointz"))
maxpoint(2) = cl.next(maxpoint(2));
std::cout << "min point = " << minpoint << std::endl;
std::cout << "max point = " << maxpoint << std::endl;
std::cout << "min normal = " << minnormal << std::endl;
std::cout << "max normal = " << maxnormal << std::endl;
bool matcholdbcid = false;
boundary_id_type oldbcid = 0;
if (cl.search("--oldbcid"))
{
matcholdbcid = true;
oldbcid = cl.next(oldbcid);
if (oldbcid < 0)
oldbcid = BoundaryInfo::invalid_id;
}
AutoPtr<FEBase> fe = FEBase::build(dim, FEType(FIRST,LAGRANGE));
QGauss qface(dim-1, CONSTANT);
fe->attach_quadrature_rule(&qface);
const std::vector<Point> &face_points = fe->get_xyz();
const std::vector<Point> &face_normals = fe->get_normals();
MeshBase::element_iterator el = mesh.elements_begin();
const MeshBase::element_iterator end_el = mesh.elements_end();
for (; el != end_el; ++el)
{
Elem *elem = *el;
unsigned int n_sides = elem->n_sides();
for (unsigned int s=0; s != n_sides; ++s)
{
if (elem->neighbor(s))
continue;
fe->reinit(elem,s);
const Point &p = face_points[0];
const Point &n = face_normals[0];
//std::cout << "elem = " << elem->id() << std::endl;
//std::cout << "centroid = " << elem->centroid() << std::endl;
//std::cout << "p = " << p << std::endl;
//std::cout << "n = " << n << std::endl;
if (p(0) > minpoint(0) && p(0) < maxpoint(0) &&
p(1) > minpoint(1) && p(1) < maxpoint(1) &&
p(2) > minpoint(2) && p(2) < maxpoint(2) &&
n(0) > minnormal(0) && n(0) < maxnormal(0) &&
n(1) > minnormal(1) && n(1) < maxnormal(1) &&
n(2) > minnormal(2) && n(2) < maxnormal(2))
{
if (matcholdbcid &&
mesh.boundary_info->boundary_id(elem, s) != oldbcid)
continue;
mesh.boundary_info->remove_side(elem, s);
mesh.boundary_info->add_side(elem, s, bcid);
//std::cout << "Set element " << elem->id() << " side " << s <<
// " to boundary " << bcid << std::endl;
}
}
}
std::string outputname;
if(cl.search("--output"))
{
outputname = cl.next("mesh.xda");
}
else
{
outputname = "new.";
outputname += meshname;
}
mesh.write(outputname.c_str());
std::cout << "Wrote mesh " << outputname << std::endl;
return 0;
}
void
MaterialPropertyStorage::prolongStatefulProps(
const std::vector<std::vector<QpMap>> & refinement_map,
QBase & qrule,
QBase & qrule_face,
MaterialPropertyStorage & parent_material_props,
MaterialData & child_material_data,
const Elem & elem,
const int input_parent_side,
const int input_child,
const int input_child_side)
{
mooseAssert(input_child != -1 || input_parent_side == input_child_side, "Invalid inputs!");
unsigned int n_qpoints = 0;
// If we passed in -1 for these then we really need to store properties at 0
unsigned int parent_side = input_parent_side == -1 ? 0 : input_parent_side;
unsigned int child_side = input_child_side == -1 ? 0 : input_child_side;
if (input_child_side == -1) // Not doing side projection (ie, doing volume projection)
n_qpoints = qrule.n_points();
else
n_qpoints = qrule_face.n_points();
child_material_data.resize(n_qpoints);
unsigned int n_children = elem.n_children();
std::vector<unsigned int> children;
if (input_child != -1) // Passed in a child explicitly
children.push_back(input_child);
else
{
children.resize(n_children);
for (unsigned int child = 0; child < n_children; child++)
children[child] = child;
}
for (const auto & child : children)
{
// If we're not projecting an internal child side, but we are projecting sides, see if this
// child is on that side
if (input_child == -1 && input_child_side != -1 && !elem.is_child_on_side(child, parent_side))
continue;
const Elem * child_elem = elem.child_ptr(child);
mooseAssert(child < refinement_map.size(), "Refinement_map vector not initialized");
const std::vector<QpMap> & child_map = refinement_map[child];
initProps(child_material_data, *child_elem, child_side, n_qpoints);
for (unsigned int i = 0; i < _stateful_prop_id_to_prop_id.size(); ++i)
{
// Copy from the parent stateful properties
for (unsigned int qp = 0; qp < refinement_map[child].size(); qp++)
{
PropertyValue * child_property = props(child_elem, child_side)[i];
mooseAssert(props().contains(&elem),
"Parent pointer is not in the MaterialProps data structure");
PropertyValue * parent_property = parent_material_props.props(&elem, parent_side)[i];
child_property->qpCopy(qp, parent_property, child_map[qp]._to);
propsOld(child_elem, child_side)[i]->qpCopy(
qp, parent_material_props.propsOld(&elem, parent_side)[i], child_map[qp]._to);
if (hasOlderProperties())
propsOlder(child_elem, child_side)[i]->qpCopy(
qp, parent_material_props.propsOlder(&elem, parent_side)[i], child_map[qp]._to);
}
}
}
}
int main (int argc, char** argv)
{
LibMeshInit init(argc, argv);
PerfMon perfmon(argv[0]);
unsigned int n_subdomains = 1;
unsigned int n_rsteps = 0;
unsigned char dim = static_cast<unsigned char>(-1); // invalid dimension
double dist_fact = 0.;
bool verbose = false;
BoundaryMeshWriteMode write_bndry = BM_DISABLED;
unsigned int convert_second_order = 0;
bool addinfelems = false;
bool triangulate = false;
bool do_quality = false;
ElemQuality quality_type = DIAGONAL;
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
InfElemBuilder::InfElemOriginValue origin_x(false, 0.);
InfElemBuilder::InfElemOriginValue origin_y(false, 0.);
InfElemBuilder::InfElemOriginValue origin_z(false, 0.);
#endif
bool x_sym=false;
bool y_sym=false;
bool z_sym=false;
std::vector<std::string> names;
std::vector<std::string> var_names;
std::vector<Number> soln;
process_cmd_line(argc, argv, names,
n_subdomains, n_rsteps, dim,
dist_fact, verbose, write_bndry,
convert_second_order,
triangulate,
do_quality,
quality_type,
addinfelems,
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
origin_x, origin_y, origin_z,
#endif
x_sym, y_sym, z_sym);
UniquePtr<Mesh> mesh_ptr;
if (dim == static_cast<unsigned char>(-1))
{
mesh_ptr.reset(new Mesh(init.comm()));
}
else
{
mesh_ptr.reset(new Mesh(init.comm(),dim));
}
Mesh& mesh = *mesh_ptr;
MeshData mesh_data(mesh);
/**
* Read the input mesh
*/
if (!names.empty())
{
/*
* activate the MeshData of the dim mesh,
* so that it can be copied to the boundary
*/
if (write_bndry == BM_WITH_MESHDATA)
{
mesh_data.activate();
if (verbose)
mesh_data.print_info();
}
mesh.read(names[0]);
if (verbose)
{
mesh.print_info();
mesh.get_boundary_info().print_summary();
}
}
else
{
libMesh::out << "No input specified." << std::endl;
return 1;
}
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
if(addinfelems)
{
if (names.size() == 3)
{
libMesh::out << "ERROR: Invalid combination: Building infinite elements " << std::endl
<< "not compatible with solution import." << std::endl;
exit(1);
}
if (write_bndry != BM_DISABLED)
{
libMesh::out << "ERROR: Invalid combination: Building infinite elements " << std::endl
<< "not compatible with writing boundary conditions." << std::endl;
exit(1);
}
/*
* Sanity checks: -X/Y/Z can only be used, when the
* corresponding coordinate is also given (using -x/y/z)
*/
if ((x_sym && !origin_x.first) || // claim x-symmetry, but x-coordinate of origin not given!
(y_sym && !origin_y.first) || // the same for y
(z_sym && !origin_z.first)) // the same for z
{
libMesh::out << "ERROR: When x-symmetry is requested using -X, then" << std::endl
<< "the option -x <coord> also has to be given." << std::endl
<< "This holds obviously for y and z, too." << std::endl;
exit(1);
}
// build infinite elements
InfElemBuilder(mesh).build_inf_elem(origin_x, origin_y, origin_z,
x_sym, y_sym, z_sym,
verbose);
if (verbose)
{
mesh.print_info();
mesh.get_boundary_info().print_summary();
}
}
// sanity check
else if((origin_x.first || origin_y.first || origin_z.first) ||
(x_sym || y_sym || z_sym))
{
libMesh::out << "ERROR: -x/-y/-z/-X/-Y/-Z is only to be used when" << std::endl
<< "the option -a is also specified!" << std::endl;
exit(1);
}
#endif
/**
* Possibly read the solution
*/
if (names.size() == 3)
LegacyXdrIO(mesh,true).read_mgf_soln(names[2],
soln,
var_names);
/**
* Maybe Triangulate
*/
// if (dim == 2 && triangulate)
if (triangulate)
{
if (verbose)
libMesh::out << "...Converting to all simplices...\n";
MeshTools::Modification::all_tri(mesh);
}
/**
* Compute Shape quality metrics
*/
if (do_quality)
{
StatisticsVector<Real> sv;
sv.reserve(mesh.n_elem());
libMesh::out << "Quality type is: " << Quality::name(quality_type) << std::endl;
// What are the quality bounds for this element?
std::pair<Real, Real> bounds = mesh.elem(0)->qual_bounds(quality_type);
libMesh::out << "Quality bounds for this element type are: (" << bounds.first
<< ", " << bounds.second << ") "
<< std::endl;
MeshBase::const_element_iterator it = mesh.active_elements_begin(),
end = mesh.active_elements_end();
for (; it != end; ++it)
{
Elem *e = *it;
sv.push_back(e->quality(quality_type));
}
const unsigned int n_bins = 10;
libMesh::out << "Avg. shape quality: " << sv.mean() << std::endl;
// Find element indices below the specified cutoff.
// These might be considered "bad" elements which need refinement.
std::vector<dof_id_type> bad_elts = sv.cut_below(0.8);
libMesh::out << "Found " << bad_elts.size()
<< " of " << mesh.n_elem()
<< " elements below the cutoff." << std::endl;
/*
for (unsigned int i=0; i<bad_elts.size(); i++)
libMesh::out << bad_elts[i] << " ";
libMesh::out << std::endl;
*/
// Compute the histogram for this distribution
std::vector<dof_id_type> histogram;
sv.histogram(histogram, n_bins);
/*
for (unsigned int i=0; i<n_bins; i++)
histogram[i] = histogram[i] / mesh.n_elem();
*/
const bool do_matlab = true;
if (do_matlab)
{
std::ofstream out ("histo.m");
out << "% This is a sample histogram plot for Matlab." << std::endl;
out << "bin_members = [" << std::endl;
for (unsigned int i=0; i<n_bins; i++)
out << static_cast<Real>(histogram[i]) / static_cast<Real>(mesh.n_elem())
<< std::endl;
out << "];" << std::endl;
std::vector<Real> bin_coords(n_bins);
const Real max = *(std::max_element(sv.begin(), sv.end()));
const Real min = *(std::min_element(sv.begin(), sv.end()));
const Real delta = (max - min) / static_cast<Real>(n_bins);
for (unsigned int i=0; i<n_bins; i++)
bin_coords[i] = min + (i * delta) + delta / 2.0 ;
out << "bin_coords = [" << std::endl;
for (unsigned int i=0; i<n_bins; i++)
out << bin_coords[i] << std::endl;
out << "];" << std::endl;
out << "bar(bin_coords, bin_members, 1);" << std::endl;
out << "hold on" << std::endl;
out << "plot (bin_coords, 0, 'kx');" << std::endl;
out << "xlabel('Quality (0=Worst, 1=Best)');" << std::endl;
out << "ylabel('Percentage of elements in each bin');" << std::endl;
out << "axis([" << min << "," << max << ",0, max(bin_members)]);" << std::endl;
out << "title('" << Quality::name(quality_type) << "');" << std::endl;
}
}
/**
* Possibly convert all linear
* elements to second-order counterparts
*/
if (convert_second_order > 0)
{
bool second_order_mode = true;
std:: string message = "Converting elements to second order counterparts";
if (convert_second_order == 2)
{
second_order_mode = false;
message += ", lower version: Quad4 -> Quad8, not Quad9";
}
else if (convert_second_order == 22)
{
second_order_mode = true;
message += ", highest version: Quad4 -> Quad9";
}
else
libmesh_error_msg("Invalid value, convert_second_order = " << convert_second_order);
if (verbose)
libMesh::out << message << std::endl;
mesh.all_second_order(second_order_mode);
if (verbose)
{
mesh.print_info();
mesh.get_boundary_info().print_summary();
}
}
#ifdef LIBMESH_ENABLE_AMR
/**
* Possibly refine the mesh
*/
if (n_rsteps > 0)
{
if (verbose)
libMesh::out << "Refining the mesh "
<< n_rsteps << " times"
<< std::endl;
MeshRefinement mesh_refinement (mesh);
mesh_refinement.uniformly_refine(n_rsteps);
if (verbose)
{
mesh.print_info();
mesh.get_boundary_info().print_summary();
}
}
/**
* Possibly distort the mesh
*/
if (dist_fact > 0.)
{
libMesh::out << "Distoring the mesh by a factor of "
<< dist_fact
<< std::endl;
MeshTools::Modification::distort(mesh,dist_fact);
};
/*
char filechar[81];
sprintf(filechar,"%s-%04d.plt", "out", 0);
std::string oname(filechar);
mesh.write(oname);
for (unsigned int step=0; step<100; step++)
{
// const Real x = .5 + .25*cos((((Real) step)/100.)*3.1415927);
// const Real y = .5 + .25*sin((((Real) step)/100.)*3.1415927);
const Real x = 2.5*cos((((Real) step)/100.)*3.1415927);
const Real y = 2.5*sin((((Real) step)/100.)*3.1415927);
const Point p(x,y);
for (unsigned int e=0; e<mesh.n_elem(); e++)
if (mesh.elem(e)->active())
mesh.elem(e)->set_refinement_flag() = -1;
for (unsigned int e=0; e<mesh.n_elem(); e++)
if (mesh.elem(e)->active())
{
const Point diff = mesh.elem(e)->centroid(mesh) - p;
if (diff.size() < .5)
{
if (mesh.elem(e)->level() < 4)
mesh.elem(e)->set_refinement_flag() = 1;
else if (mesh.elem(e)->level() == 4)
mesh.elem(e)->set_refinement_flag() = 0;
}
}
mesh.mesh_refinement.refine_and_coarsen_elements();
char filechar[81];
sprintf(filechar,"%s-%04d.plt", "out", step+1);
std::string oname(filechar);
mesh.write(oname);
}
*/
#endif
// /**
// * Possibly partition the mesh
// */
if (n_subdomains > 1)
mesh.partition(n_subdomains);
/**
* Possibly write the mesh
*/
{
if (names.size() >= 2)
{
/*
* When the mesh got refined, it is likely that
* the user does _not_ want to write also
* the coarse elements, but only the active ones.
* Use Mesh::create_submesh() to create a mesh
* of only active elements, and then write _this_
* new mesh.
*/
if (n_rsteps > 0)
{
if (verbose)
libMesh::out << " Mesh got refined, will write only _active_ elements." << std::endl;
Mesh new_mesh (init.comm(), mesh.mesh_dimension());
construct_mesh_of_active_elements(new_mesh, mesh);
// now write the new_mesh
if (names.size() == 2)
new_mesh.write(names[1]);
else if (names.size() == 3)
new_mesh.write(names[1], soln, var_names);
else
libmesh_error_msg("Invalid names.size() = " << names.size());
}
else
{
if (names.size() == 2)
mesh.write(names[1]);
else if (names.size() == 3)
mesh.write(names[1], soln, var_names);
else
libmesh_error_msg("Invalid names.size() = " << names.size());
}
/**
* Possibly write the BCs
*/
if (write_bndry != BM_DISABLED)
{
BoundaryMesh boundary_mesh
(mesh.comm(), cast_int<unsigned char>(mesh.mesh_dimension()-1));
MeshData boundary_mesh_data (boundary_mesh);
std::string boundary_name = "bndry_";
boundary_name += names[1];
if (write_bndry == BM_MESH_ONLY)
mesh.get_boundary_info().sync(boundary_mesh);
else if (write_bndry == BM_WITH_MESHDATA)
mesh.get_boundary_info().sync(boundary_mesh, &boundary_mesh_data, &mesh_data);
else
libmesh_error_msg("Invalid value write_bndry = " << write_bndry);
if (names.size() == 2)
boundary_mesh.write(boundary_name);
else if (names.size() == 3)
boundary_mesh.write(boundary_name, soln, var_names);
}
}
};
/*
libMesh::out << "Infinite loop, look at memory footprint" << std::endl;
for (;;)
;
*/
return 0;
}
// Begin the main program.
int main (int argc, char ** argv)
{
// Initialize libMesh, like in example 2.
LibMeshInit init (argc, argv);
// This example requires Infinite Elements
#ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
libmesh_example_requires(false, "--enable-ifem");
#else
// Skip this 3D example if libMesh was compiled as 1D/2D-only.
libmesh_example_requires(3 <= LIBMESH_DIM, "3D support");
// Tell the user what we are doing.
libMesh::out << "Running ex6 with dim = 3" << std::endl << std::endl;
// Create a serialized mesh, distributed across the default MPI
// communicator.
// InfElemBuilder still requires some updates to be DistributedMesh
// compatible
ReplicatedMesh mesh(init.comm());
// Use the internal mesh generator to create elements
// on the square [-1,1]^3, of type Hex8.
MeshTools::Generation::build_cube (mesh,
4, 4, 4,
-1., 1.,
-1., 1.,
-1., 1.,
HEX8);
// Print information about the mesh to the screen.
mesh.print_info();
// Write the mesh before the infinite elements are added
#ifdef LIBMESH_HAVE_EXODUS_API
ExodusII_IO(mesh).write ("orig_mesh.e");
#endif
// Normally, when a mesh is imported or created in
// libMesh, only conventional elements exist. The infinite
// elements used here, however, require prescribed
// nodal locations (with specified distances from an imaginary
// origin) and configurations that a conventional mesh creator
// in general does not offer. Therefore, an efficient method
// for building infinite elements is offered. It can account
// for symmetry planes and creates infinite elements in a fully
// automatic way.
//
// Right now, the simplified interface is used, automatically
// determining the origin. Check MeshBase for a generalized
// method that can even return the element faces of interior
// vibrating surfaces. The bool determines whether to be
// verbose.
InfElemBuilder builder(mesh);
builder.build_inf_elem(true);
// Reassign subdomain_id() of all infinite elements.
// Otherwise, the exodus-api will fail on the mesh.
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
if(elem->infinite())
{
elem->subdomain_id() = 1;
}
}
// Print information about the mesh to the screen.
mesh.print_info();
// Write the mesh with the infinite elements added.
// Compare this to the original mesh.
#ifdef LIBMESH_HAVE_EXODUS_API
ExodusII_IO(mesh).write ("ifems_added.e");
#endif
// After building infinite elements, we have to let
// the elements find their neighbors again.
mesh.find_neighbors();
// Create an equation systems object, where ThinSystem
// offers only the crucial functionality for solving a
// system. Use ThinSystem when you want the sleekest
// system possible.
EquationSystems equation_systems (mesh);
// Declare the system and its variables.
// Create a system named "Wave". This can
// be a simple, steady system
equation_systems.add_system<LinearImplicitSystem> ("Wave");
// Create an FEType describing the approximation
// characteristics of the InfFE object. Note that
// the constructor automatically defaults to some
// sensible values. But use FIRST order
// approximation.
FEType fe_type(FIRST);
// Add the variable "p" to "Wave". Note that there exist
// various approaches in adding variables. In example 3,
// add_variable took the order of approximation and used
// default values for the FEFamily, while here the FEType
// is used.
equation_systems.get_system("Wave").add_variable("p", fe_type);
// Give the system a pointer to the matrix assembly
// function.
equation_systems.get_system("Wave").attach_assemble_function (assemble_wave);
// Set the speed of sound and fluid density
// as EquationSystems parameter,
// so that assemble_wave() can access it.
equation_systems.parameters.set<Real>("speed") = 1.;
equation_systems.parameters.set<Real>("fluid density") = 1.;
// Initialize the data structures for the equation system.
equation_systems.init();
// Prints information about the system to the screen.
equation_systems.print_info();
// Solve the system "Wave".
equation_systems.get_system("Wave").solve();
// Write the whole EquationSystems object to file.
// For infinite elements, the concept of nodal_soln()
// is not applicable. Therefore, writing the mesh in
// some format @e always gives all-zero results at
// the nodes of the infinite elements. Instead,
// use the FEInterface::compute_data() methods to
// determine physically correct results within an
// infinite element.
equation_systems.write ("eqn_sys.dat", WRITE);
// All done.
return 0;
#endif // else part of ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
}
void ParmetisPartitioner::build_graph (const MeshBase & mesh)
{
// build the graph in distributed CSR format. Note that
// the edges in the graph will correspond to
// face neighbors
const dof_id_type n_active_local_elem = mesh.n_active_local_elem();
// If we have boundary elements in this mesh, we want to account for
// the connectivity between them and interior elements. We can find
// interior elements from boundary elements, but we need to build up
// a lookup map to do the reverse.
typedef LIBMESH_BEST_UNORDERED_MULTIMAP<const Elem *, const Elem *>
map_type;
map_type interior_to_boundary_map;
{
MeshBase::const_element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::const_element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
// If we don't have an interior_parent then there's nothing to look us
// up.
if ((elem->dim() >= LIBMESH_DIM) ||
!elem->interior_parent())
continue;
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
// FIXME - non-const versions of the Elem set methods
// would be nice
Elem * neighbor = const_cast<Elem *>(*n_it);
#if defined(LIBMESH_HAVE_UNORDERED_MULTIMAP) || \
defined(LIBMESH_HAVE_TR1_UNORDERED_MAP) || \
defined(LIBMESH_HAVE_HASH_MAP) || \
defined(LIBMESH_HAVE_EXT_HASH_MAP)
interior_to_boundary_map.insert
(std::make_pair(neighbor, elem));
#else
interior_to_boundary_map.insert
(interior_to_boundary_map.begin(),
std::make_pair(neighbor, elem));
#endif
}
}
}
#ifdef LIBMESH_ENABLE_AMR
std::vector<const Elem *> neighbors_offspring;
#endif
std::vector<std::vector<dof_id_type> > graph(n_active_local_elem);
dof_id_type graph_size=0;
const dof_id_type first_local_elem = _pmetis->vtxdist[mesh.processor_id()];
MeshBase::const_element_iterator elem_it = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator elem_end = mesh.active_local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
libmesh_assert (_global_index_by_pid_map.count(elem->id()));
const dof_id_type global_index_by_pid =
_global_index_by_pid_map[elem->id()];
const dof_id_type local_index =
global_index_by_pid - first_local_elem;
libmesh_assert_less (local_index, n_active_local_elem);
std::vector<dof_id_type> & graph_row = graph[local_index];
// Loop over the element's neighbors. An element
// adjacency corresponds to a face neighbor
for (unsigned int ms=0; ms<elem->n_neighbors(); ms++)
{
const Elem * neighbor = elem->neighbor(ms);
if (neighbor != libmesh_nullptr)
{
// If the neighbor is active treat it
// as a connection
if (neighbor->active())
{
libmesh_assert(_global_index_by_pid_map.count(neighbor->id()));
const dof_id_type neighbor_global_index_by_pid =
_global_index_by_pid_map[neighbor->id()];
graph_row.push_back(neighbor_global_index_by_pid);
graph_size++;
}
#ifdef LIBMESH_ENABLE_AMR
// Otherwise we need to find all of the
// neighbor's children that are connected to
// us and add them
else
{
// The side of the neighbor to which
// we are connected
const unsigned int ns =
neighbor->which_neighbor_am_i (elem);
libmesh_assert_less (ns, neighbor->n_neighbors());
// Get all the active children (& grandchildren, etc...)
// of the neighbor
// FIXME - this is the wrong thing, since we
// should be getting the active family tree on
// our side only. But adding too many graph
// links may cause hanging nodes to tend to be
// on partition interiors, which would reduce
// communication overhead for constraint
// equations, so we'll leave it.
neighbor->active_family_tree (neighbors_offspring);
// Get all the neighbor's children that
// live on that side and are thus connected
// to us
for (unsigned int nc=0; nc<neighbors_offspring.size(); nc++)
{
const Elem * child =
neighbors_offspring[nc];
// This does not assume a level-1 mesh.
// Note that since children have sides numbered
// coincident with the parent then this is a sufficient test.
if (child->neighbor(ns) == elem)
{
libmesh_assert (child->active());
libmesh_assert (_global_index_by_pid_map.count(child->id()));
const dof_id_type child_global_index_by_pid =
_global_index_by_pid_map[child->id()];
graph_row.push_back(child_global_index_by_pid);
graph_size++;
}
}
}
#endif /* ifdef LIBMESH_ENABLE_AMR */
}
}
if ((elem->dim() < LIBMESH_DIM) &&
elem->interior_parent())
{
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
// FIXME - non-const versions of the Elem set methods
// would be nice
Elem * neighbor = const_cast<Elem *>(*n_it);
const dof_id_type neighbor_global_index_by_pid =
_global_index_by_pid_map[neighbor->id()];
graph_row.push_back(neighbor_global_index_by_pid);
graph_size++;
}
}
// Check for any boundary neighbors
typedef map_type::iterator map_it_type;
std::pair<map_it_type, map_it_type>
bounds = interior_to_boundary_map.equal_range(elem);
for (map_it_type it = bounds.first; it != bounds.second; ++it)
{
const Elem * neighbor = it->second;
const dof_id_type neighbor_global_index_by_pid =
_global_index_by_pid_map[neighbor->id()];
graph_row.push_back(neighbor_global_index_by_pid);
graph_size++;
}
}
// Reserve space in the adjacency array
_pmetis->xadj.clear();
_pmetis->xadj.reserve (n_active_local_elem + 1);
_pmetis->adjncy.clear();
_pmetis->adjncy.reserve (graph_size);
for (std::size_t r=0; r<graph.size(); r++)
{
_pmetis->xadj.push_back(_pmetis->adjncy.size());
std::vector<dof_id_type> graph_row; // build this emtpy
graph_row.swap(graph[r]); // this will deallocate at the end of scope
_pmetis->adjncy.insert(_pmetis->adjncy.end(),
graph_row.begin(),
graph_row.end());
}
// The end of the adjacency array for the last elem
_pmetis->xadj.push_back(_pmetis->adjncy.size());
libmesh_assert_equal_to (_pmetis->xadj.size(), n_active_local_elem+1);
libmesh_assert_equal_to (_pmetis->adjncy.size(), graph_size);
}
void setUp() {
#if LIBMESH_DIM > 2
mesh.reset(new Mesh(*TestCommWorld));
MeshTools::Generation::build_cube(*mesh, 1, 1, 1);
es.reset(new EquationSystems(*mesh));
sys = &(es->add_system<System> ("SimpleSystem"));
sys->add_variable("x2");
sys->add_variable("x3");
sys->add_variable("c05");
sys->add_variable("y4");
sys->add_variable("xy");
sys->add_variable("yz");
sys->add_variable("xyz");
es->init();
NumericVector<Number> & sol = *sys->solution;
Elem *elem = mesh->query_elem_ptr(0);
if (elem && elem->processor_id() == TestCommWorld->rank())
{
// Set x2 = 2*x
sol.set(elem->node_ref(1).dof_number(0,0,0), 2);
sol.set(elem->node_ref(2).dof_number(0,0,0), 2);
sol.set(elem->node_ref(5).dof_number(0,0,0), 2);
sol.set(elem->node_ref(6).dof_number(0,0,0), 2);
// Set x3 = 3*x
sol.set(elem->node_ref(1).dof_number(0,1,0), 3);
sol.set(elem->node_ref(2).dof_number(0,1,0), 3);
sol.set(elem->node_ref(5).dof_number(0,1,0), 3);
sol.set(elem->node_ref(6).dof_number(0,1,0), 3);
// Set c05 = 0.5
sol.set(elem->node_ref(0).dof_number(0,2,0), 0.5);
sol.set(elem->node_ref(1).dof_number(0,2,0), 0.5);
sol.set(elem->node_ref(2).dof_number(0,2,0), 0.5);
sol.set(elem->node_ref(3).dof_number(0,2,0), 0.5);
sol.set(elem->node_ref(4).dof_number(0,2,0), 0.5);
sol.set(elem->node_ref(5).dof_number(0,2,0), 0.5);
sol.set(elem->node_ref(6).dof_number(0,2,0), 0.5);
sol.set(elem->node_ref(7).dof_number(0,2,0), 0.5);
// Set y4 = 4*y
sol.set(elem->node_ref(2).dof_number(0,3,0), 4);
sol.set(elem->node_ref(3).dof_number(0,3,0), 4);
sol.set(elem->node_ref(6).dof_number(0,3,0), 4);
sol.set(elem->node_ref(7).dof_number(0,3,0), 4);
// Set xy = x*y
sol.set(elem->node_ref(2).dof_number(0,4,0), 1);
sol.set(elem->node_ref(6).dof_number(0,4,0), 1);
// Set yz = y*z
sol.set(elem->node_ref(6).dof_number(0,5,0), 1);
sol.set(elem->node_ref(7).dof_number(0,5,0), 1);
// Set xyz = x*y*z
sol.set(elem->node_ref(6).dof_number(0,6,0), 1);
}
sol.close();
sys->update();
c.reset(new FEMContext(*sys));
s.reset(new FEMContext(*sys));
if (elem && elem->processor_id() == TestCommWorld->rank())
{
c->pre_fe_reinit(*sys, elem);
c->elem_fe_reinit();
s->pre_fe_reinit(*sys, elem);
s->side = 3;
s->side_fe_reinit();
}
#endif
}
void unpack(std::vector<int>::const_iterator in,
Elem** out,
MeshBase* mesh)
{
#ifndef NDEBUG
const std::vector<int>::const_iterator original_in = in;
const int incoming_header = *in++;
libmesh_assert (incoming_header == elem_magic_header);
#endif
// int 0: level
const unsigned int level =
static_cast<unsigned int>(*in++);
#ifdef LIBMESH_ENABLE_AMR
// int 1: p level
const unsigned int p_level =
static_cast<unsigned int>(*in++);
// int 2: refinement flag
const int rflag = *in++;
libmesh_assert(rflag >= 0);
libmesh_assert(rflag < Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState refinement_flag =
static_cast<Elem::RefinementState>(rflag);
// int 3: p refinement flag
const int pflag = *in++;
libmesh_assert(pflag >= 0);
libmesh_assert(pflag < Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState p_refinement_flag =
static_cast<Elem::RefinementState>(pflag);
#else
in += 3;
#endif // LIBMESH_ENABLE_AMR
// int 4: element type
const int typeint = *in++;
libmesh_assert(typeint >= 0);
libmesh_assert(typeint < INVALID_ELEM);
const ElemType type =
static_cast<ElemType>(typeint);
const unsigned int n_nodes =
Elem::type_to_n_nodes_map[type];
// int 5: processor id
const unsigned int processor_id =
static_cast<unsigned int>(*in++);
libmesh_assert (processor_id < libMesh::n_processors() ||
processor_id == DofObject::invalid_processor_id);
// int 6: subdomain id
const unsigned int subdomain_id =
static_cast<unsigned int>(*in++);
// int 7: dof object id
const unsigned int id =
static_cast<unsigned int>(*in++);
libmesh_assert (id != DofObject::invalid_id);
#ifdef LIBMESH_ENABLE_AMR
// int 8: parent dof object id
const unsigned int parent_id =
static_cast<unsigned int>(*in++);
libmesh_assert (level == 0 || parent_id != DofObject::invalid_id);
libmesh_assert (level != 0 || parent_id == DofObject::invalid_id);
// int 9: local child id
const unsigned int which_child_am_i =
static_cast<unsigned int>(*in++);
#else
in += 2;
#endif // LIBMESH_ENABLE_AMR
// Make sure we don't miscount above when adding the "magic" header
// plus the real data header
libmesh_assert(in - original_in == header_size + 1);
Elem *elem = mesh->query_elem(id);
// if we already have this element, make sure its
// properties match, and update any missing neighbor
// links, but then go on
if (elem)
{
libmesh_assert (elem->level() == level);
libmesh_assert (elem->id() == id);
libmesh_assert (elem->processor_id() == processor_id);
libmesh_assert (elem->subdomain_id() == subdomain_id);
libmesh_assert (elem->type() == type);
libmesh_assert (elem->n_nodes() == n_nodes);
#ifndef NDEBUG
// All our nodes should be correct
for (unsigned int i=0; i != n_nodes; ++i)
libmesh_assert(elem->node(i) ==
static_cast<unsigned int>(*in++));
#else
in += n_nodes;
#endif
#ifdef LIBMESH_ENABLE_AMR
libmesh_assert (elem->p_level() == p_level);
libmesh_assert (elem->refinement_flag() == refinement_flag);
libmesh_assert (elem->p_refinement_flag() == p_refinement_flag);
libmesh_assert (!level || elem->parent() != NULL);
libmesh_assert (!level || elem->parent()->id() == parent_id);
libmesh_assert (!level || elem->parent()->child(which_child_am_i) == elem);
#endif
// Our neighbor links should be "close to" correct - we may have
// to update them, but we can check for some inconsistencies.
for (unsigned int n=0; n != elem->n_neighbors(); ++n)
{
const unsigned int neighbor_id =
static_cast<unsigned int>(*in++);
// If the sending processor sees a domain boundary here,
// we'd better agree.
if (neighbor_id == DofObject::invalid_id)
{
libmesh_assert(elem->neighbor(n) == NULL);
continue;
}
// If the sending processor has a remote_elem neighbor here,
// then all we know is that we'd better *not* have a domain
// boundary.
if (neighbor_id == remote_elem->id())
{
libmesh_assert(elem->neighbor(n) != NULL);
continue;
}
Elem *neigh = mesh->query_elem(neighbor_id);
// The sending processor sees a neighbor here, so if we
// don't have that neighboring element, then we'd better
// have a remote_elem signifying that fact.
if (!neigh)
{
libmesh_assert(elem->neighbor(n) == remote_elem);
continue;
}
// The sending processor has a neighbor here, and we have
// that element, but that does *NOT* mean we're already
// linking to it. Perhaps we initially received both elem
// and neigh from processors on which their mutual link was
// remote?
libmesh_assert(elem->neighbor(n) == neigh ||
elem->neighbor(n) == remote_elem);
// If the link was originally remote, we should update it,
// and make sure the appropriate parts of its family link
// back to us.
if (elem->neighbor(n) == remote_elem)
{
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
}
// FIXME: We should add some debug mode tests to ensure that the
// encoded indexing and boundary conditions are consistent.
}
else
{
// We don't already have the element, so we need to create it.
// Find the parent if necessary
Elem *parent = NULL;
#ifdef LIBMESH_ENABLE_AMR
// Find a child element's parent
if (level > 0)
{
// Note that we must be very careful to construct the send
// connectivity so that parents are encountered before
// children. If we get here and can't find the parent that
// is a fatal error.
parent = mesh->elem(parent_id);
}
// Or assert that the sending processor sees no parent
else
libmesh_assert (parent_id == static_cast<unsigned int>(-1));
#else
// No non-level-0 elements without AMR
libmesh_assert (level == 0);
#endif
elem = Elem::build(type,parent).release();
libmesh_assert (elem);
#ifdef LIBMESH_ENABLE_AMR
if (level != 0)
{
// Since this is a newly created element, the parent must
// have previously thought of this child as a remote element.
libmesh_assert (parent->child(which_child_am_i) == remote_elem);
parent->add_child(elem, which_child_am_i);
}
// Assign the refinement flags and levels
elem->set_p_level(p_level);
elem->set_refinement_flag(refinement_flag);
elem->set_p_refinement_flag(p_refinement_flag);
libmesh_assert (elem->level() == level);
// If this element definitely should have children, assign
// remote_elem to all of them for now, for consistency. Later
// unpacked elements may overwrite that.
if (!elem->active())
for (unsigned int c=0; c != elem->n_children(); ++c)
elem->add_child(const_cast<RemoteElem*>(remote_elem), c);
#endif // LIBMESH_ENABLE_AMR
// Assign the IDs
elem->subdomain_id() = subdomain_id;
elem->processor_id() = processor_id;
elem->set_id() = id;
// Assign the connectivity
libmesh_assert (elem->n_nodes() == n_nodes);
for (unsigned int n=0; n != n_nodes; n++)
elem->set_node(n) =
mesh->node_ptr
(static_cast<unsigned int>(*in++));
for (unsigned int n=0; n<elem->n_neighbors(); n++)
{
const unsigned int neighbor_id =
static_cast<unsigned int>(*in++);
if (neighbor_id == DofObject::invalid_id)
continue;
// We may be unpacking an element that was a ghost element on the
// sender, in which case the element's neighbors may not all be
// known by the packed element. We'll have to set such
// neighbors to remote_elem ourselves and wait for a later
// packed element to give us better information.
if (neighbor_id == remote_elem->id())
{
elem->set_neighbor(n, const_cast<RemoteElem*>(remote_elem));
continue;
}
// If we don't have the neighbor element, then it's a
// remote_elem until we get it.
Elem *neigh = mesh->query_elem(neighbor_id);
if (!neigh)
{
elem->set_neighbor(n, const_cast<RemoteElem*>(remote_elem));
continue;
}
// If we have the neighbor element, then link to it, and
// make sure the appropriate parts of its family link back
// to us.
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
elem->unpack_indexing(in);
}
in += elem->packed_indexing_size();
// If this is a coarse element,
// add any element side boundary condition ids
if (level == 0)
for (unsigned int s = 0; s != elem->n_sides(); ++s)
{
const int num_bcs = *in++;
libmesh_assert (num_bcs >= 0);
for(int bc_it=0; bc_it < num_bcs; bc_it++)
mesh->boundary_info->add_side (elem, s, *in++);
}
// Return the new element
*out = elem;
}
UniquePtr<Elem> InfHex8::build_side (const unsigned int i,
bool proxy) const
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
switch (i)
{
// base
case 0:
return UniquePtr<Elem>(new Side<Quad4,InfHex8>(this,i));
// ifem sides
case 1:
case 2:
case 3:
case 4:
return UniquePtr<Elem>(new Side<InfQuad4,InfHex8>(this,i));
default:
libmesh_error_msg("Invalid side i = " << i);
}
}
else
{
// Create NULL pointer to be initialized, returned later.
Elem * face = libmesh_nullptr;
// Think of a unit cube: (-1,1) x (-1,1) x (1,1)
switch (i)
{
case 0: // the base face
{
face = new Quad4;
break;
}
// connecting to another infinite element
case 1:
case 2:
case 3:
case 4:
{
face = new InfQuad4;
break;
}
default:
libmesh_error_msg("Invalid side i = " << i);
}
face->subdomain_id() = this->subdomain_id();
// Set the nodes
for (unsigned n=0; n<face->n_nodes(); ++n)
face->set_node(n) = this->get_node(InfHex8::side_nodes_map[i][n]);
return UniquePtr<Elem>(face);
}
libmesh_error_msg("We'll never get here!");
return UniquePtr<Elem>();
}
Elem *
Packing<Elem *>::unpack (std::vector<largest_id_type>::const_iterator in,
MeshBase * mesh)
{
#ifndef NDEBUG
const std::vector<largest_id_type>::const_iterator original_in = in;
const largest_id_type incoming_header = *in++;
libmesh_assert_equal_to (incoming_header, elem_magic_header);
#endif
// int 0: level
const unsigned int level =
cast_int<unsigned int>(*in++);
#ifdef LIBMESH_ENABLE_AMR
// int 1: p level
const unsigned int p_level =
cast_int<unsigned int>(*in++);
// int 2: refinement flag and encoded has_children
const int rflag = cast_int<int>(*in++);
const int invalid_rflag =
cast_int<int>(Elem::INVALID_REFINEMENTSTATE);
libmesh_assert_greater_equal (rflag, 0);
libmesh_assert_less (rflag, invalid_rflag*2+1);
const bool has_children = (rflag > invalid_rflag);
const Elem::RefinementState refinement_flag = has_children ?
cast_int<Elem::RefinementState>(rflag - invalid_rflag - 1) :
cast_int<Elem::RefinementState>(rflag);
// int 3: p refinement flag
const int pflag = cast_int<int>(*in++);
libmesh_assert_greater_equal (pflag, 0);
libmesh_assert_less (pflag, Elem::INVALID_REFINEMENTSTATE);
const Elem::RefinementState p_refinement_flag =
cast_int<Elem::RefinementState>(pflag);
#else
in += 3;
#endif // LIBMESH_ENABLE_AMR
// int 4: element type
const int typeint = cast_int<int>(*in++);
libmesh_assert_greater_equal (typeint, 0);
libmesh_assert_less (typeint, INVALID_ELEM);
const ElemType type =
cast_int<ElemType>(typeint);
const unsigned int n_nodes =
Elem::type_to_n_nodes_map[type];
// int 5: processor id
const processor_id_type processor_id =
cast_int<processor_id_type>(*in++);
libmesh_assert (processor_id < mesh->n_processors() ||
processor_id == DofObject::invalid_processor_id);
// int 6: subdomain id
const subdomain_id_type subdomain_id =
cast_int<subdomain_id_type>(*in++);
// int 7: dof object id
const dof_id_type id =
cast_int<dof_id_type>(*in++);
libmesh_assert_not_equal_to (id, DofObject::invalid_id);
#ifdef LIBMESH_ENABLE_UNIQUE_ID
// int 8: dof object unique id
const unique_id_type unique_id =
cast_int<unique_id_type>(*in++);
#endif
#ifdef LIBMESH_ENABLE_AMR
// int 9: parent dof object id.
// Note: If level==0, then (*in) == invalid_id. In
// this case, the equality check in cast_int<unsigned>(*in) will
// never succeed. Therefore, we should only attempt the more
// rigorous cast verification in cases where level != 0.
const dof_id_type parent_id =
(level == 0)
? static_cast<dof_id_type>(*in++)
: cast_int<dof_id_type>(*in++);
libmesh_assert (level == 0 || parent_id != DofObject::invalid_id);
libmesh_assert (level != 0 || parent_id == DofObject::invalid_id);
// int 10: local child id
// Note: If level==0, then which_child_am_i is not valid, so don't
// do the more rigorous cast verification.
const unsigned int which_child_am_i =
(level == 0)
? static_cast<unsigned int>(*in++)
: cast_int<unsigned int>(*in++);
#else
in += 2;
#endif // LIBMESH_ENABLE_AMR
const dof_id_type interior_parent_id =
static_cast<dof_id_type>(*in++);
// Make sure we don't miscount above when adding the "magic" header
// plus the real data header
libmesh_assert_equal_to (in - original_in, header_size + 1);
Elem * elem = mesh->query_elem_ptr(id);
// if we already have this element, make sure its
// properties match, and update any missing neighbor
// links, but then go on
if (elem)
{
libmesh_assert_equal_to (elem->level(), level);
libmesh_assert_equal_to (elem->id(), id);
//#ifdef LIBMESH_ENABLE_UNIQUE_ID
// No check for unique id sanity
//#endif
libmesh_assert_equal_to (elem->processor_id(), processor_id);
libmesh_assert_equal_to (elem->subdomain_id(), subdomain_id);
libmesh_assert_equal_to (elem->type(), type);
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
#ifndef NDEBUG
// All our nodes should be correct
for (unsigned int i=0; i != n_nodes; ++i)
libmesh_assert(elem->node_id(i) ==
cast_int<dof_id_type>(*in++));
#else
in += n_nodes;
#endif
#ifdef LIBMESH_ENABLE_AMR
libmesh_assert_equal_to (elem->refinement_flag(), refinement_flag);
libmesh_assert_equal_to (elem->has_children(), has_children);
#ifdef DEBUG
if (elem->active())
{
libmesh_assert_equal_to (elem->p_level(), p_level);
libmesh_assert_equal_to (elem->p_refinement_flag(), p_refinement_flag);
}
#endif
libmesh_assert (!level || elem->parent() != libmesh_nullptr);
libmesh_assert (!level || elem->parent()->id() == parent_id);
libmesh_assert (!level || elem->parent()->child_ptr(which_child_am_i) == elem);
#endif
// Our interior_parent link should be "close to" correct - we
// may have to update it, but we can check for some
// inconsistencies.
{
// If the sending processor sees no interior_parent here, we'd
// better agree.
if (interior_parent_id == DofObject::invalid_id)
{
if (elem->dim() < LIBMESH_DIM)
libmesh_assert (!(elem->interior_parent()));
}
// If the sending processor has a remote_elem interior_parent,
// then all we know is that we'd better have *some*
// interior_parent
else if (interior_parent_id == remote_elem->id())
{
libmesh_assert(elem->interior_parent());
}
else
{
Elem * ip = mesh->query_elem_ptr(interior_parent_id);
// The sending processor sees an interior parent here, so
// if we don't have that interior element, then we'd
// better have a remote_elem signifying that fact.
if (!ip)
libmesh_assert_equal_to (elem->interior_parent(), remote_elem);
else
{
// The sending processor has an interior_parent here,
// and we have that element, but that does *NOT* mean
// we're already linking to it. Perhaps we initially
// received elem from a processor on which the
// interior_parent link was remote?
libmesh_assert(elem->interior_parent() == ip ||
elem->interior_parent() == remote_elem);
// If the link was originally remote, update it
if (elem->interior_parent() == remote_elem)
{
elem->set_interior_parent(ip);
}
}
}
}
// Our neighbor links should be "close to" correct - we may have
// to update a remote_elem link, and we can check for possible
// inconsistencies along the way.
//
// For subactive elements, we don't bother keeping neighbor
// links in good shape, so there's nothing we need to set or can
// safely assert here.
if (!elem->subactive())
for (auto n : elem->side_index_range())
{
const dof_id_type neighbor_id =
cast_int<dof_id_type>(*in++);
// If the sending processor sees a domain boundary here,
// we'd better agree.
if (neighbor_id == DofObject::invalid_id)
{
libmesh_assert (!(elem->neighbor_ptr(n)));
continue;
}
// If the sending processor has a remote_elem neighbor here,
// then all we know is that we'd better *not* have a domain
// boundary.
if (neighbor_id == remote_elem->id())
{
libmesh_assert(elem->neighbor_ptr(n));
continue;
}
Elem * neigh = mesh->query_elem_ptr(neighbor_id);
// The sending processor sees a neighbor here, so if we
// don't have that neighboring element, then we'd better
// have a remote_elem signifying that fact.
if (!neigh)
{
libmesh_assert_equal_to (elem->neighbor_ptr(n), remote_elem);
continue;
}
// The sending processor has a neighbor here, and we have
// that element, but that does *NOT* mean we're already
// linking to it. Perhaps we initially received both elem
// and neigh from processors on which their mutual link was
// remote?
libmesh_assert(elem->neighbor_ptr(n) == neigh ||
elem->neighbor_ptr(n) == remote_elem);
// If the link was originally remote, we should update it,
// and make sure the appropriate parts of its family link
// back to us.
if (elem->neighbor_ptr(n) == remote_elem)
{
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
}
// Our p level and refinement flags should be "close to" correct
// if we're not an active element - we might have a p level
// increased or decreased by changes in remote_elem children.
//
// But if we have remote_elem children, then we shouldn't be
// doing a projection on this inactive element on this
// processor, so we won't need correct p settings. Couldn't
// hurt to update, though.
#ifdef LIBMESH_ENABLE_AMR
if (elem->processor_id() != mesh->processor_id())
{
elem->hack_p_level(p_level);
elem->set_p_refinement_flag(p_refinement_flag);
}
#endif // LIBMESH_ENABLE_AMR
// FIXME: We should add some debug mode tests to ensure that the
// encoded indexing and boundary conditions are consistent.
}
else
{
// We don't already have the element, so we need to create it.
// Find the parent if necessary
Elem * parent = libmesh_nullptr;
#ifdef LIBMESH_ENABLE_AMR
// Find a child element's parent
if (level > 0)
{
// Note that we must be very careful to construct the send
// connectivity so that parents are encountered before
// children. If we get here and can't find the parent that
// is a fatal error.
parent = mesh->elem_ptr(parent_id);
}
// Or assert that the sending processor sees no parent
else
libmesh_assert_equal_to (parent_id, DofObject::invalid_id);
#else
// No non-level-0 elements without AMR
libmesh_assert_equal_to (level, 0);
#endif
elem = Elem::build(type,parent).release();
libmesh_assert (elem);
#ifdef LIBMESH_ENABLE_AMR
if (level != 0)
{
// Since this is a newly created element, the parent must
// have previously thought of this child as a remote element.
libmesh_assert_equal_to (parent->child_ptr(which_child_am_i), remote_elem);
parent->add_child(elem, which_child_am_i);
}
// Assign the refinement flags and levels
elem->set_p_level(p_level);
elem->set_refinement_flag(refinement_flag);
elem->set_p_refinement_flag(p_refinement_flag);
libmesh_assert_equal_to (elem->level(), level);
// If this element should have children, assign remote_elem to
// all of them for now, for consistency. Later unpacked
// elements may overwrite that.
if (has_children)
{
const unsigned int nc = elem->n_children();
for (unsigned int c=0; c != nc; ++c)
elem->add_child(const_cast<RemoteElem *>(remote_elem), c);
}
#endif // LIBMESH_ENABLE_AMR
// Assign the IDs
elem->subdomain_id() = subdomain_id;
elem->processor_id() = processor_id;
elem->set_id() = id;
#ifdef LIBMESH_ENABLE_UNIQUE_ID
elem->set_unique_id() = unique_id;
#endif
// Assign the connectivity
libmesh_assert_equal_to (elem->n_nodes(), n_nodes);
for (unsigned int n=0; n != n_nodes; n++)
elem->set_node(n) =
mesh->node_ptr
(cast_int<dof_id_type>(*in++));
// Set interior_parent if found
{
// We may be unpacking an element that was a ghost element on the
// sender, in which case the element's interior_parent may not be
// known by the packed element. We'll have to set such
// interior_parents to remote_elem ourselves and wait for a
// later packed element to give us better information.
if (interior_parent_id == remote_elem->id())
{
elem->set_interior_parent
(const_cast<RemoteElem *>(remote_elem));
}
else if (interior_parent_id != DofObject::invalid_id)
{
// If we don't have the interior parent element, then it's
// a remote_elem until we get it.
Elem * ip = mesh->query_elem_ptr(interior_parent_id);
if (!ip )
elem->set_interior_parent
(const_cast<RemoteElem *>(remote_elem));
else
elem->set_interior_parent(ip);
}
}
for (auto n : elem->side_index_range())
{
const dof_id_type neighbor_id =
cast_int<dof_id_type>(*in++);
if (neighbor_id == DofObject::invalid_id)
continue;
// We may be unpacking an element that was a ghost element on the
// sender, in which case the element's neighbors may not all be
// known by the packed element. We'll have to set such
// neighbors to remote_elem ourselves and wait for a later
// packed element to give us better information.
if (neighbor_id == remote_elem->id())
{
elem->set_neighbor(n, const_cast<RemoteElem *>(remote_elem));
continue;
}
// If we don't have the neighbor element, then it's a
// remote_elem until we get it.
Elem * neigh = mesh->query_elem_ptr(neighbor_id);
if (!neigh)
{
elem->set_neighbor(n, const_cast<RemoteElem *>(remote_elem));
continue;
}
// If we have the neighbor element, then link to it, and
// make sure the appropriate parts of its family link back
// to us.
elem->set_neighbor(n, neigh);
elem->make_links_to_me_local(n);
}
elem->unpack_indexing(in);
}
in += elem->packed_indexing_size();
// If this is a coarse element,
// add any element side or edge boundary condition ids
if (level == 0)
{
for (auto s : elem->side_index_range())
{
const boundary_id_type num_bcs =
cast_int<boundary_id_type>(*in++);
for (boundary_id_type bc_it=0; bc_it < num_bcs; bc_it++)
mesh->get_boundary_info().add_side
(elem, s, cast_int<boundary_id_type>(*in++));
}
for (auto e : elem->edge_index_range())
{
const boundary_id_type num_bcs =
cast_int<boundary_id_type>(*in++);
for (boundary_id_type bc_it=0; bc_it < num_bcs; bc_it++)
mesh->get_boundary_info().add_edge
(elem, e, cast_int<boundary_id_type>(*in++));
}
for (unsigned short sf=0; sf != 2; ++sf)
{
const boundary_id_type num_bcs =
cast_int<boundary_id_type>(*in++);
for (boundary_id_type bc_it=0; bc_it < num_bcs; bc_it++)
mesh->get_boundary_info().add_shellface
(elem, sf, cast_int<boundary_id_type>(*in++));
}
}
// Return the new element
return elem;
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_edge (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
// Maps holding the maximum element level that touches an edge
std::map<std::pair<unsigned int, unsigned int>, unsigned char>
max_level_at_edge;
std::map<std::pair<unsigned int, unsigned int>, unsigned char>
max_p_level_at_edge;
// Loop over all the active elements & fill the maps
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem* elem = *elem_it;
const unsigned char elem_level =
elem->level() + ((elem->refinement_flag() == Elem::REFINE) ? 1 : 0);
const unsigned char elem_p_level =
elem->p_level() + ((elem->p_refinement_flag() == Elem::REFINE) ? 1 : 0);
// Set the max_level at each edge
for (unsigned int n=0; n<elem->n_edges(); n++)
{
AutoPtr<Elem> edge = elem->build_edge(n);
unsigned int childnode0 = edge->node(0);
unsigned int childnode1 = edge->node(1);
if (childnode1 < childnode0)
std::swap(childnode0, childnode1);
for (const Elem *p = elem; p != NULL; p = p->parent())
{
AutoPtr<Elem> pedge = p->build_edge(n);
unsigned int node0 = pedge->node(0);
unsigned int node1 = pedge->node(1);
if (node1 < node0)
std::swap(node0, node1);
// If elem does not share this edge with its ancestor
// p, refinement levels of elements sharing p's edge
// are not restricted by refinement levels of elem.
// Furthermore, elem will not share this edge with any
// of p's ancestors, so we can safely break out of the
// for loop early.
if (node0 != childnode0 && node1 != childnode1)
break;
childnode0 = node0;
childnode1 = node1;
std::pair<unsigned int, unsigned int> edge_key =
std::make_pair(node0, node1);
if (max_level_at_edge.find(edge_key) ==
max_level_at_edge.end())
{
max_level_at_edge[edge_key] = elem_level;
max_p_level_at_edge[edge_key] = elem_p_level;
}
else
{
max_level_at_edge[edge_key] =
std::max (max_level_at_edge[edge_key], elem_level);
max_p_level_at_edge[edge_key] =
std::max (max_p_level_at_edge[edge_key], elem_p_level);
}
}
}
}
}
// Now loop over the active elements and flag the elements
// who violate the requested level mismatch
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
const unsigned int elem_level = elem->level();
const unsigned int elem_p_level = elem->p_level();
// Skip the element if it is already fully flagged
if (elem->refinement_flag() == Elem::REFINE &&
elem->p_refinement_flag() == Elem::REFINE)
continue;
// Loop over the nodes, check for possible mismatch
for (unsigned int n=0; n<elem->n_edges(); n++)
{
AutoPtr<Elem> edge = elem->build_edge(n);
unsigned int node0 = edge->node(0);
unsigned int node1 = edge->node(1);
if (node1 < node0)
std::swap(node0, node1);
std::pair<unsigned int, unsigned int> edge_key =
std::make_pair(node0, node1);
// Flag the element for refinement if it violates
// the requested level mismatch
if ( (elem_level + max_mismatch) < max_level_at_edge[edge_key]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ( (elem_p_level + max_mismatch) < max_p_level_at_edge[edge_key]
&& elem->p_refinement_flag() != Elem::REFINE)
{
elem->set_p_refinement_flag (Elem::REFINE);
flags_changed = true;
}
}
}
}
// If flags changed on any processor then they changed globally
CommWorld.max(flags_changed);
return flags_changed;
}
void add_cube_convex_hull_to_mesh(MeshBase& mesh, Point lower_limit, Point upper_limit)
{
#ifdef LIBMESH_HAVE_TETGEN
SerialMesh cube_mesh(3);
unsigned n_elem = 1;
MeshTools::Generation::build_cube(cube_mesh,
n_elem,n_elem,n_elem, // n. elements in each direction
lower_limit(0), upper_limit(0),
lower_limit(1), upper_limit(1),
lower_limit(2), upper_limit(2),
HEX8);
// The pointset_convexhull() algorithm will ignore the Hex8s
// in the Mesh, and just construct the triangulation
// of the convex hull.
TetGenMeshInterface t(cube_mesh);
t.pointset_convexhull();
// Now add all nodes from the boundary of the cube_mesh to the input mesh.
// Map from "node id in cube_mesh" -> "node id in mesh". Initially inserted
// with a dummy value, later to be assigned a value by the input mesh.
std::map<unsigned,unsigned> node_id_map;
typedef std::map<unsigned,unsigned>::iterator iterator;
{
MeshBase::element_iterator it = cube_mesh.elements_begin();
const MeshBase::element_iterator end = cube_mesh.elements_end();
for ( ; it != end; ++it)
{
Elem* elem = *it;
for (unsigned s=0; s<elem->n_sides(); ++s)
if (elem->neighbor(s) == NULL)
{
// Add the node IDs of this side to the set
AutoPtr<Elem> side = elem->side(s);
for (unsigned n=0; n<side->n_nodes(); ++n)
node_id_map.insert( std::make_pair(side->node(n), /*dummy_value=*/0) );
}
}
}
// For each node in the map, insert it into the input mesh and keep
// track of the ID assigned.
for (iterator it=node_id_map.begin(); it != node_id_map.end(); ++it)
{
// Id of the node in the cube mesh
unsigned id = (*it).first;
// Pointer to node in the cube mesh
Node* old_node = cube_mesh.node_ptr(id);
// Add geometric point to input mesh
Node* new_node = mesh.add_point ( *old_node );
// Track ID value of new_node in map
(*it).second = new_node->id();
}
// With the points added and the map data structure in place, we are
// ready to add each TRI3 element of the cube_mesh to the input Mesh
// with proper node assignments
{
MeshBase::element_iterator el = cube_mesh.elements_begin();
const MeshBase::element_iterator end_el = cube_mesh.elements_end();
for (; el != end_el; ++el)
{
Elem* old_elem = *el;
if (old_elem->type() == TRI3)
{
Elem* new_elem = mesh.add_elem(new Tri3);
// Assign nodes in new elements. Since this is an example,
// we'll do it in several steps.
for (unsigned i=0; i<old_elem->n_nodes(); ++i)
{
// Locate old node ID in the map
iterator it = node_id_map.find(old_elem->node(i));
// Check for not found
if (it == node_id_map.end())
{
libMesh::err << "Node id " << old_elem->node(i) << " not found in map!" << std::endl;
libmesh_error();
}
// Mapping to node ID in input mesh
unsigned new_node_id = (*it).second;
// Node pointer assigned from input mesh
new_elem->set_node(i) = mesh.node_ptr(new_node_id);
}
}
}
}
#endif // LIBMESH_HAVE_TETGEN
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_node (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
// Vector holding the maximum element level that touches a node.
std::vector<unsigned char> max_level_at_node (_mesh.n_nodes(), 0);
std::vector<unsigned char> max_p_level_at_node (_mesh.n_nodes(), 0);
// Loop over all the active elements & fill the vector
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem* elem = *elem_it;
const unsigned char elem_level =
elem->level() + ((elem->refinement_flag() == Elem::REFINE) ? 1 : 0);
const unsigned char elem_p_level =
elem->p_level() + ((elem->p_refinement_flag() == Elem::REFINE) ? 1 : 0);
// Set the max_level at each node
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const unsigned int node_number = elem->node(n);
libmesh_assert_less (node_number, max_level_at_node.size());
max_level_at_node[node_number] =
std::max (max_level_at_node[node_number], elem_level);
max_p_level_at_node[node_number] =
std::max (max_p_level_at_node[node_number], elem_p_level);
}
}
}
// Now loop over the active elements and flag the elements
// who violate the requested level mismatch
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
const unsigned int elem_level = elem->level();
const unsigned int elem_p_level = elem->p_level();
// Skip the element if it is already fully flagged
if (elem->refinement_flag() == Elem::REFINE &&
elem->p_refinement_flag() == Elem::REFINE)
continue;
// Loop over the nodes, check for possible mismatch
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const unsigned int node_number = elem->node(n);
// Flag the element for refinement if it violates
// the requested level mismatch
if ( (elem_level + max_mismatch) < max_level_at_node[node_number]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ( (elem_p_level + max_mismatch) < max_p_level_at_node[node_number]
&& elem->p_refinement_flag() != Elem::REFINE)
{
elem->set_p_refinement_flag (Elem::REFINE);
flags_changed = true;
}
}
}
}
// If flags changed on any processor then they changed globally
CommWorld.max(flags_changed);
return flags_changed;
}
void VTKIO::cells_to_vtk()
{
const MeshBase& mesh = MeshOutput<MeshBase>::mesh();
vtkSmartPointer<vtkCellArray> cells = vtkSmartPointer<vtkCellArray>::New();
vtkSmartPointer<vtkIdList> pts = vtkSmartPointer<vtkIdList>::New();
std::vector<int> types(mesh.n_active_local_elem());
unsigned active_element_counter = 0;
vtkSmartPointer<vtkIntArray> elem_id = vtkSmartPointer<vtkIntArray>::New();
elem_id->SetName("libmesh_elem_id");
elem_id->SetNumberOfComponents(1);
vtkSmartPointer<vtkIntArray> subdomain_id = vtkSmartPointer<vtkIntArray>::New();
subdomain_id->SetName("subdomain_id");
subdomain_id->SetNumberOfComponents(1);
MeshBase::const_element_iterator it = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end = mesh.active_local_elements_end();
for (; it != end; ++it, ++active_element_counter)
{
Elem *elem = *it;
pts->SetNumberOfIds(elem->n_nodes());
// get the connectivity for this element
std::vector<dof_id_type> conn;
elem->connectivity(0, VTK, conn);
for (unsigned int i=0; i<conn.size(); ++i)
{
// If the node ID is not found in the _local_node_map, we'll
// add it to the _vtk_grid. NOTE[JWP]: none of the examples
// I have actually enters this section of code...
if (_local_node_map.find(conn[i]) == _local_node_map.end())
{
dof_id_type global_node_id = elem->node(i);
const Node* the_node = mesh.node_ptr(global_node_id);
// Error checking...
if (the_node == NULL)
{
libMesh::err << "Error getting pointer to node "
<< global_node_id
<< "!" << std::endl;
libmesh_error();
}
// InsertNextPoint accepts either a double or float array of length 3.
Real pt[3] = {0., 0., 0.};
for (unsigned int d=0; d<LIBMESH_DIM; ++d)
pt[d] = (*the_node)(d);
// Insert the point into the _vtk_grid
vtkIdType local = _vtk_grid->GetPoints()->InsertNextPoint(pt);
// Update the _local_node_map with the ID returned by VTK
_local_node_map[global_node_id] = local;
}
// Otherwise, the node ID was found in the _local_node_map, so
// insert it into the vtkIdList.
pts->InsertId(i, _local_node_map[conn[i]]);
}
vtkIdType vtkcellid = cells->InsertNextCell(pts);
types[active_element_counter] = this->get_elem_type(elem->type());
elem_id->InsertTuple1(vtkcellid, elem->id());
subdomain_id->InsertTuple1(vtkcellid, elem->subdomain_id());
} // end loop over active elements
_vtk_grid->SetCells(&types[0], cells);
_vtk_grid->GetCellData()->AddArray(elem_id);
_vtk_grid->GetCellData()->AddArray(subdomain_id);
}