bool MeshRefinement::limit_overrefined_boundary(const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_object_only();
bool flags_changed = false;
// Loop over all the active elements & look for mismatches to fix.
{
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;
// If we don't have an interior_parent then there's nothing to
// be mismatched with.
if ((elem->dim() >= LIBMESH_DIM) ||
!elem->interior_parent())
continue;
const unsigned char elem_level =
cast_int<unsigned char>(elem->level() +
((elem->refinement_flag() == Elem::REFINE) ? 1 : 0));
const unsigned char elem_p_level =
cast_int<unsigned char>(elem->p_level() +
((elem->p_refinement_flag() == Elem::REFINE) ? 1 : 0));
// 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 (((elem_level - max_mismatch) >
neighbor->level()) &&
(neighbor->refinement_flag() != Elem::REFINE))
{
neighbor->set_refinement_flag(Elem::REFINE);
flags_changed = true;
}
if (((elem_p_level + 1 - max_mismatch) >
neighbor->p_level()) &&
(neighbor->p_refinement_flag() != Elem::REFINE))
{
neighbor->set_p_refinement_flag(Elem::REFINE);
flags_changed = true;
}
} // loop over interior neighbors
}
}
return flags_changed;
}
void ElemCutter::operator()(const Elem & elem,
const std::vector<Real> & vertex_distance_func)
{
libmesh_assert_equal_to (vertex_distance_func.size(), elem.n_vertices());
_inside_elem.clear();
_outside_elem.clear();
// check for quick return?
{
// completely outside?
if (this->is_outside(elem, vertex_distance_func))
{
//std::cout << "element completely outside\n";
_outside_elem.push_back(& elem);
return;
}
// completely inside?
else if (this->is_inside(elem, vertex_distance_func))
{
//std::cout << "element completely inside\n";
_inside_elem.push_back(&elem);
return;
}
libmesh_assert (this->is_cut (elem, vertex_distance_func));
}
// we now know we are in a cut element, find the intersecting points.
this->find_intersection_points (elem, vertex_distance_func);
// and then dispatch the proper method
switch (elem.dim())
{
case 1: this->cut_1D(elem, vertex_distance_func); break;
case 2: this->cut_2D(elem, vertex_distance_func); break;
case 3: this->cut_3D(elem, vertex_distance_func); break;
default: libmesh_error_msg("Invalid element dimension: " << elem.dim());
}
}
void QComposite<QSubCell>::init (const Elem &elem,
const std::vector<Real> &vertex_distance_func,
unsigned int p_level)
{
libmesh_assert_equal_to (vertex_distance_func.size(), elem.n_vertices());
libmesh_assert_equal_to (_dim, elem.dim());
// if we are not cut, revert to simple base class init() method.
if (!_elem_cutter.is_cut (elem, vertex_distance_func))
{
_q_subcell.init (elem.type(), p_level);
_points = _q_subcell.get_points();
_weights = _q_subcell.get_weights();
//this->print_info();
return;
}
// Get a pointer to the element's reference element. We want to
// perform cutting on the reference element such that the quadrature
// point locations of the subelements live in the reference
// coordinate system, thereby eliminating the need for inverse
// mapping.
const Elem *reference_elem = elem.reference_elem();
libmesh_assert (reference_elem != NULL);
_elem_cutter(*reference_elem, vertex_distance_func);
//_elem_cutter(elem, vertex_distance_func);
// clear our state & accumulate points from subelements
_points.clear();
_weights.clear();
// inside subelem
{
const std::vector<Elem const*> &inside_elem (_elem_cutter.inside_elements());
std::cout << inside_elem.size() << " elements inside\n";
this->add_subelem_values(inside_elem);
}
// outside subelem
{
const std::vector<Elem const*> &outside_elem (_elem_cutter.outside_elements());
std::cout << outside_elem.size() << " elements outside\n";
this->add_subelem_values(outside_elem);
}
this->print_info();
}
void LinearElasticityWithContact::move_mesh (MeshBase & input_mesh,
const NumericVector<Number> & input_solution)
{
// Maintain a set of node ids that we've encountered.
LIBMESH_BEST_UNORDERED_SET<dof_id_type> encountered_node_ids;
// Localize input_solution so that we have the data to move all
// elements (not just elements local to this processor).
UniquePtr< NumericVector<Number> > localized_input_solution =
NumericVector<Number>::build(input_solution.comm());
localized_input_solution->init (input_solution.size(), false, SERIAL);
input_solution.localize(*localized_input_solution);
MeshBase::const_element_iterator el = input_mesh.active_elements_begin();
const MeshBase::const_element_iterator end_el = input_mesh.active_elements_end();
for ( ; el != end_el; ++el)
{
Elem * elem = *el;
Elem * orig_elem = _sys.get_mesh().elem_ptr(elem->id());
for (unsigned int node_id=0; node_id<elem->n_nodes(); node_id++)
{
Node & node = elem->node_ref(node_id);
if (encountered_node_ids.find(node.id()) != encountered_node_ids.end())
continue;
encountered_node_ids.insert(node.id());
std::vector<std::string> uvw_names(3);
uvw_names[0] = "u";
uvw_names[1] = "v";
uvw_names[2] = "w";
{
const Point master_point = elem->master_point(node_id);
Point uvw;
for (unsigned int index=0; index<uvw_names.size(); index++)
{
const unsigned int var = _sys.variable_number(uvw_names[index]);
const FEType & fe_type = _sys.get_dof_map().variable_type(var);
FEComputeData data (_sys.get_equation_systems(), master_point);
FEInterface::compute_data(elem->dim(),
fe_type,
elem,
data);
std::vector<dof_id_type> dof_indices_var;
_sys.get_dof_map().dof_indices (orig_elem, dof_indices_var, var);
for (unsigned int i=0; i<dof_indices_var.size(); i++)
{
Number value = (*localized_input_solution)(dof_indices_var[i]) * data.shape[i];
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
// We explicitly store the real part in uvw
uvw(index) += value.real();
#else
uvw(index) += value;
#endif
}
}
// Update the node's location
node += uvw;
}
}
}
}
void ExodusII_IO::read (const std::string& fname)
{
// This is a serial-only process for now;
// the Mesh should be read on processor 0 and
// broadcast later
// libmesh_assert_equal_to (libMesh::processor_id(), 0);
#ifndef LIBMESH_HAVE_EXODUS_API
libMesh::err << "ERROR, ExodusII API is not defined.\n"
<< "Input file " << fname << " cannot be read"
<< std::endl;
libmesh_error();
#else
// 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
ExodusII_IO_Helper::ElementMaps em; // Instantiate the ElementMaps interface
exio_helper->open(fname.c_str()); // Open the exodus file, if possible
exio_helper->read_header(); // Get header information from exodus file
exio_helper->print_header(); // Print header information
//assertion fails due to inconsistent mesh dimension
// libmesh_assert_equal_to (static_cast<unsigned int>(exio_helper->get_num_dim()), mesh.mesh_dimension()); // Be sure number of dimensions
// is equal to the number of
// dimensions in the mesh supplied.
exio_helper->read_nodes(); // Read nodes from the exodus file
mesh.reserve_nodes(exio_helper->get_num_nodes()); // Reserve space for the nodes.
// Loop over the nodes, create Nodes with local processor_id 0.
for (int i=0; i<exio_helper->get_num_nodes(); i++)
mesh.add_point (Point(exio_helper->get_x(i),
exio_helper->get_y(i),
exio_helper->get_z(i)), i);
libmesh_assert_equal_to (static_cast<unsigned int>(exio_helper->get_num_nodes()), mesh.n_nodes());
exio_helper->read_block_info(); // Get information about all the blocks
mesh.reserve_elem(exio_helper->get_num_elem()); // Reserve space for the elements
// Read in the element connectivity for each block.
int nelem_last_block = 0;
std::map<int, unsigned int> exodus_id_to_mesh_id;
// Loop over all the blocks
for (int i=0; i<exio_helper->get_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
mesh.subdomain_name(static_cast<subdomain_id_type>(subdomain_id)) =
exio_helper->get_block_name(i);
// 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);
//if (_verbose)
//libMesh::out << "Reading a block of " << type_str << " elements." << std::endl;
// Loop over all the faces in this block
int jmax = nelem_last_block+exio_helper->get_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) ;
//elem->set_id(j);// Don't try to second guess the Element ID setting scheme!
elems_of_dimension[elem->dim()] = true;
elem = mesh.add_elem (elem); // Catch the Elem pointer that the Mesh throws back
exodus_id_to_mesh_id[j+1] = elem->id();
// Set all the nodes for this element
for (int k=0; k<exio_helper->get_num_nodes_per_elem(); k++)
{
int gi = (j-nelem_last_block)*exio_helper->get_num_nodes_per_elem() + conv.get_node_map(k); // global index
int node_number = exio_helper->get_connect(gi); // Global node number (1-based)
elem->set_node(k) = mesh.node_ptr((node_number-1)); // Set node number
// Subtract 1 since
// exodus is internally 1-based
}
}
// running sum of # of elements per block,
// (should equal total number of elements in the end)
nelem_last_block += exio_helper->get_num_elem_this_blk();
}
libmesh_assert_equal_to (static_cast<unsigned int>(nelem_last_block), mesh.n_elem());
// 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);
// Read in sideset information -- this is useful for applying boundary conditions
{
exio_helper->read_sideset_info(); // Get basic information about ALL sidesets
int offset=0;
for (int i=0; i<exio_helper->get_num_side_sets(); i++)
{
offset += (i > 0 ? exio_helper->get_num_sides_per_set(i-1) : 0); // Compute new offset
exio_helper->read_sideset (i, offset);
mesh.boundary_info->sideset_name(exio_helper->get_side_set_id(i)) =
exio_helper->get_side_set_name(i);
}
const std::vector<int>& elem_list = exio_helper->get_elem_list();
const std::vector<int>& side_list = exio_helper->get_side_list();
const std::vector<int>& id_list = exio_helper->get_id_list();
for (unsigned int e=0; e<elem_list.size(); e++)
{
// Set any relevant node/edge maps for this element
Elem * elem = mesh.elem(exodus_id_to_mesh_id[elem_list[e]]);
const ExodusII_IO_Helper::Conversion conv =
em.assign_conversion(elem->type());
mesh.boundary_info->add_side (exodus_id_to_mesh_id[elem_list[e]],
conv.get_side_map(side_list[e]-1),
id_list[e]);
}
}
// Read nodeset info
{
exio_helper->read_nodeset_info();
for (int nodeset=0; nodeset<exio_helper->get_num_node_sets(); nodeset++)
{
int nodeset_id = exio_helper->get_nodeset_id(nodeset);
mesh.boundary_info->nodeset_name(nodeset_id) =
exio_helper->get_node_set_name(nodeset);
exio_helper->read_nodeset(nodeset);
const std::vector<int>& node_list = exio_helper->get_node_list();
for(unsigned int node=0; node<node_list.size(); node++)
mesh.boundary_info->add_node(node_list[node]-1, nodeset_id);
}
}
#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
}
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 UnstructuredMesh::find_neighbors (const bool reset_remote_elements,
const bool reset_current_list)
{
// We might actually want to run this on an empty mesh
// (e.g. the boundary mesh for a nonexistant bcid!)
// libmesh_assert_not_equal_to (this->n_nodes(), 0);
// libmesh_assert_not_equal_to (this->n_elem(), 0);
// This function must be run on all processors at once
parallel_object_only();
LOG_SCOPE("find_neighbors()", "Mesh");
const element_iterator el_end = this->elements_end();
//TODO:[BSK] This should be removed later?!
if (reset_current_list)
for (element_iterator el = this->elements_begin(); el != el_end; ++el)
{
Elem * e = *el;
for (unsigned int s=0; s<e->n_neighbors(); s++)
if (e->neighbor_ptr(s) != remote_elem ||
reset_remote_elements)
e->set_neighbor(s, libmesh_nullptr);
}
// Find neighboring elements by first finding elements
// with identical side keys and then check to see if they
// are neighbors
{
// data structures -- Use the hash_multimap if available
typedef unsigned int key_type;
typedef std::pair<Elem *, unsigned char> val_type;
typedef std::pair<key_type, val_type> key_val_pair;
typedef LIBMESH_BEST_UNORDERED_MULTIMAP<key_type, val_type> map_type;
// A map from side keys to corresponding elements & side numbers
map_type side_to_elem_map;
for (element_iterator el = this->elements_begin(); el != el_end; ++el)
{
Elem * element = *el;
for (unsigned char ms=0; ms<element->n_neighbors(); ms++)
{
next_side:
// If we haven't yet found a neighbor on this side, try.
// Even if we think our neighbor is remote, that
// information may be out of date.
if (element->neighbor_ptr(ms) == libmesh_nullptr ||
element->neighbor_ptr(ms) == remote_elem)
{
// Get the key for the side of this element
const unsigned int key = element->key(ms);
// Look for elements that have an identical side key
std::pair <map_type::iterator, map_type::iterator>
bounds = side_to_elem_map.equal_range(key);
// May be multiple keys, check all the possible
// elements which _might_ be neighbors.
if (bounds.first != bounds.second)
{
// Get the side for this element
const UniquePtr<Elem> my_side(element->side_ptr(ms));
// Look at all the entries with an equivalent key
while (bounds.first != bounds.second)
{
// Get the potential element
Elem * neighbor = bounds.first->second.first;
// Get the side for the neighboring element
const unsigned int ns = bounds.first->second.second;
const UniquePtr<Elem> their_side(neighbor->side_ptr(ns));
//libmesh_assert(my_side.get());
//libmesh_assert(their_side.get());
// If found a match with my side
//
// We need special tests here for 1D:
// since parents and children have an equal
// side (i.e. a node), we need to check
// ns != ms, and we also check level() to
// avoid setting our neighbor pointer to
// any of our neighbor's descendants
if( (*my_side == *their_side) &&
(element->level() == neighbor->level()) &&
((element->dim() != 1) || (ns != ms)) )
{
// So share a side. Is this a mixed pair
// of subactive and active/ancestor
// elements?
// If not, then we're neighbors.
// If so, then the subactive's neighbor is
if (element->subactive() ==
neighbor->subactive())
{
// an element is only subactive if it has
// been coarsened but not deleted
element->set_neighbor (ms,neighbor);
neighbor->set_neighbor(ns,element);
}
else if (element->subactive())
{
element->set_neighbor(ms,neighbor);
}
else if (neighbor->subactive())
{
neighbor->set_neighbor(ns,element);
}
side_to_elem_map.erase (bounds.first);
// get out of this nested crap
goto next_side;
}
++bounds.first;
}
}
// didn't find a match...
// Build the map entry for this element
key_val_pair kvp;
kvp.first = key;
kvp.second.first = element;
kvp.second.second = ms;
// use the lower bound as a hint for
// where to put it.
#if defined(LIBMESH_HAVE_UNORDERED_MAP) || defined(LIBMESH_HAVE_TR1_UNORDERED_MAP) || defined(LIBMESH_HAVE_HASH_MAP) || defined(LIBMESH_HAVE_EXT_HASH_MAP)
side_to_elem_map.insert (kvp);
#else
side_to_elem_map.insert (bounds.first,kvp);
#endif
}
}
}
}
#ifdef LIBMESH_ENABLE_AMR
/**
* Here we look at all of the child elements which
* don't already have valid neighbors.
*
* If a child element has a NULL neighbor it is
* either because it is on the boundary or because
* its neighbor is at a different level. In the
* latter case we must get the neighbor from the
* parent.
*
* If a child element has a remote_elem neighbor
* on a boundary it shares with its parent, that
* info may have become out-dated through coarsening
* of the neighbor's parent. In this case, if the
* parent's neighbor is active then the child should
* share it.
*
* Furthermore, that neighbor better be active,
* otherwise we missed a child somewhere.
*
*
* We also need to look through children ordered by increasing
* refinement level in order to add new interior_parent() links in
* boundary elements which have just been generated by refinement,
* and fix links in boundary elements whose previous
* interior_parent() has just been coarsened away.
*/
const unsigned int n_levels = MeshTools::n_levels(*this);
for (unsigned int level = 1; level < n_levels; ++level)
{
element_iterator end = this->level_elements_end(level);
for (element_iterator el = this->level_elements_begin(level);
el != end; ++el)
{
Elem * current_elem = *el;
libmesh_assert(current_elem);
Elem * parent = current_elem->parent();
libmesh_assert(parent);
const unsigned int my_child_num = parent->which_child_am_i(current_elem);
for (unsigned int s=0; s < current_elem->n_neighbors(); s++)
{
if (current_elem->neighbor_ptr(s) == libmesh_nullptr ||
(current_elem->neighbor_ptr(s) == remote_elem &&
parent->is_child_on_side(my_child_num, s)))
{
Elem * neigh = parent->neighbor_ptr(s);
// If neigh was refined and had non-subactive children
// made remote earlier, then a non-subactive elem should
// actually have one of those remote children as a
// neighbor
if (neigh && (neigh->ancestor()) && (!current_elem->subactive()))
{
#ifdef DEBUG
// Let's make sure that "had children made remote"
// situation is actually the case
libmesh_assert(neigh->has_children());
bool neigh_has_remote_children = false;
for (unsigned int c = 0; c != neigh->n_children(); ++c)
{
if (neigh->child_ptr(c) == remote_elem)
neigh_has_remote_children = true;
}
libmesh_assert(neigh_has_remote_children);
// And let's double-check that we don't have
// a remote_elem neighboring a local element
libmesh_assert_not_equal_to (current_elem->processor_id(),
this->processor_id());
#endif // DEBUG
neigh = const_cast<RemoteElem *>(remote_elem);
}
if (!current_elem->subactive())
current_elem->set_neighbor(s, neigh);
#ifdef DEBUG
if (neigh != libmesh_nullptr && neigh != remote_elem)
// We ignore subactive elements here because
// we don't care about neighbors of subactive element.
if ((!neigh->active()) && (!current_elem->subactive()))
{
libMesh::err << "On processor " << this->processor_id()
<< std::endl;
libMesh::err << "Bad element ID = " << current_elem->id()
<< ", Side " << s << ", Bad neighbor ID = " << neigh->id() << std::endl;
libMesh::err << "Bad element proc_ID = " << current_elem->processor_id()
<< ", Bad neighbor proc_ID = " << neigh->processor_id() << std::endl;
libMesh::err << "Bad element size = " << current_elem->hmin()
<< ", Bad neighbor size = " << neigh->hmin() << std::endl;
libMesh::err << "Bad element center = " << current_elem->centroid()
<< ", Bad neighbor center = " << neigh->centroid() << std::endl;
libMesh::err << "ERROR: "
<< (current_elem->active()?"Active":"Ancestor")
<< " Element at level "
<< current_elem->level() << std::endl;
libMesh::err << "with "
<< (parent->active()?"active":
(parent->subactive()?"subactive":"ancestor"))
<< " parent share "
<< (neigh->subactive()?"subactive":"ancestor")
<< " neighbor at level " << neigh->level()
<< std::endl;
NameBasedIO(*this).write ("bad_mesh.gmv");
libmesh_error_msg("Problematic mesh written to bad_mesh.gmv.");
}
#endif // DEBUG
}
}
// We can skip to the next element if we're full-dimension
// and therefore don't have any interior parents
if (current_elem->dim() >= LIBMESH_DIM)
continue;
// We have no interior parents unless we can find one later
current_elem->set_interior_parent(libmesh_nullptr);
Elem * pip = parent->interior_parent();
if (!pip)
continue;
// If there's no interior_parent children, whether due to a
// remote element or a non-conformity, then there's no
// children to search.
if (pip == remote_elem || pip->active())
{
current_elem->set_interior_parent(pip);
continue;
}
// For node comparisons we'll need a sensible tolerance
Real node_tolerance = current_elem->hmin() * TOLERANCE;
// Otherwise our interior_parent should be a child of our
// parent's interior_parent.
for (unsigned int c=0; c != pip->n_children(); ++c)
{
Elem * child = pip->child_ptr(c);
// If we have a remote_elem, that might be our
// interior_parent. We'll set it provisionally now and
// keep trying to find something better.
if (child == remote_elem)
{
current_elem->set_interior_parent
(const_cast<RemoteElem *>(remote_elem));
continue;
}
bool child_contains_our_nodes = true;
for (unsigned int n=0; n != current_elem->n_nodes();
++n)
{
bool child_contains_this_node = false;
for (unsigned int cn=0; cn != child->n_nodes();
++cn)
if (child->point(cn).absolute_fuzzy_equals
(current_elem->point(n), node_tolerance))
{
child_contains_this_node = true;
break;
}
if (!child_contains_this_node)
{
child_contains_our_nodes = false;
break;
}
}
if (child_contains_our_nodes)
{
current_elem->set_interior_parent(child);
break;
}
}
// We should have found *some* interior_parent at this
// point, whether semilocal or remote.
libmesh_assert(current_elem->interior_parent());
}
}
#endif // AMR
#ifdef DEBUG
MeshTools::libmesh_assert_valid_neighbors(*this,
!reset_remote_elements);
MeshTools::libmesh_assert_valid_amr_interior_parents(*this);
#endif
}
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);
// 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 != libmesh_nullptr)
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);
// Get the libMesh element type corresponding to this VTK element type.
ElemType libmesh_elem_type = _element_maps.find(cell->GetCellType());
Elem * elem = Elem::build(libmesh_elem_type).release();
// 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(cast_int<dof_id_type>(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 char 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_error_msg("Cannot open dimension " \
<< mesh.mesh_dimension() \
<< " mesh file when configured without " \
<< mesh.mesh_dimension() \
<< "D support.");
#endif // LIBMESH_DIM < 3
}
void CheckpointIO::read_connectivity (Xdr & io)
{
// convenient reference to our mesh
MeshBase & mesh = MeshInput<MeshBase>::mesh();
unsigned int n_active_levels;
io.data(n_active_levels, "# n_active_levels");
// Keep track of the highest dimensional element we've added to the mesh
unsigned int highest_elem_dim = 1;
for(unsigned int level=0; level < n_active_levels; level++)
{
xdr_id_type n_elem_at_level = 0;
io.data (n_elem_at_level, "");
for (unsigned int i=0; i<n_elem_at_level; i++)
{
// id type pid subdomain_id parent_id
std::vector<largest_id_type> elem_data(5);
io.data_stream
(&elem_data[0], cast_int<unsigned int>(elem_data.size()),
cast_int<unsigned int>(elem_data.size()));
#ifdef LIBMESH_ENABLE_UNIQUE_ID
largest_id_type unique_id = 0;
io.data(unique_id, "# unique id");
#endif
#ifdef LIBMESH_ENABLE_AMR
unsigned int p_level = 0;
io.data(p_level, "# p_level");
#endif
unsigned int n_nodes = Elem::type_to_n_nodes_map[elem_data[1]];
// Snag the node ids this element was connected to
std::vector<largest_id_type> conn_data(n_nodes);
io.data_stream
(&conn_data[0], cast_int<unsigned int>(conn_data.size()),
cast_int<unsigned int>(conn_data.size()));
const dof_id_type id =
cast_int<dof_id_type> (elem_data[0]);
const ElemType elem_type =
static_cast<ElemType> (elem_data[1]);
const processor_id_type proc_id =
cast_int<processor_id_type>(elem_data[2]);
const subdomain_id_type subdomain_id =
cast_int<subdomain_id_type>(elem_data[3]);
const dof_id_type parent_id =
cast_int<dof_id_type> (elem_data[4]);
Elem * parent =
(parent_id == DofObject::invalid_processor_id) ?
libmesh_nullptr : mesh.elem_ptr(parent_id);
// Create the element
Elem * elem = Elem::build(elem_type, parent).release();
#ifdef LIBMESH_ENABLE_UNIQUE_ID
elem->set_unique_id() = unique_id;
#endif
if(elem->dim() > highest_elem_dim)
highest_elem_dim = elem->dim();
elem->set_id() = id;
elem->processor_id() = proc_id;
elem->subdomain_id() = subdomain_id;
#ifdef LIBMESH_ENABLE_AMR
elem->hack_p_level(p_level);
// Set parent connections
if(parent)
{
parent->add_child(elem);
parent->set_refinement_flag (Elem::INACTIVE);
elem->set_refinement_flag (Elem::JUST_REFINED);
}
#endif
libmesh_assert(elem->n_nodes() == conn_data.size());
// Connect all the nodes to this element
for (unsigned int n=0; n<conn_data.size(); n++)
elem->set_node(n) =
mesh.node_ptr(cast_int<dof_id_type>(conn_data[n]));
mesh.add_elem(elem);
}
}
mesh.set_mesh_dimension(cast_int<unsigned char>(highest_elem_dim));
}
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;
}
}
}
}
}
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;
}
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
}