void
SystemBase::augmentSendList(std::vector<dof_id_type> & send_list)
{
std::set<dof_id_type> & ghosted_elems = _subproblem.ghostedElems();
DofMap & dof_map = dofMap();
std::vector<dof_id_type> dof_indices;
System & sys = system();
unsigned int sys_num = sys.number();
unsigned int n_vars = sys.n_vars();
for (std::set<dof_id_type>::iterator elem_id = ghosted_elems.begin();
elem_id != ghosted_elems.end();
++elem_id)
{
Elem * elem = _mesh.elem(*elem_id);
if (elem->active())
{
dof_map.dof_indices(elem, dof_indices);
for (unsigned int i=0; i<dof_indices.size(); i++)
{
dof_id_type dof = dof_indices[i];
// Only need to ghost it if it's actually not on this processor
if (dof < dof_map.first_dof() || dof >= dof_map.end_dof())
send_list.push_back(dof);
}
// Now add the DoFs from all of the nodes. This is necessary because of block
// restricted variables. A variable might not live _on_ this element but it
// might live on nodes connected to this element.
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
Node * node = elem->get_node(n);
// Have to get each variable's dofs
for (unsigned int v=0; v<n_vars; v++)
{
const Variable & var = sys.variable(v);
unsigned int var_num = var.number();
unsigned int n_comp = var.n_components();
// See if this variable has any dofs at this node
if (node->n_dofs(sys_num, var_num) > 0)
{
// Loop over components of the variable
for (unsigned int c=0; c<n_comp; c++)
send_list.push_back(node->dof_number(sys_num, var_num, c));
}
}
}
}
}
}
// Begin the main program.
int main (int argc, char ** argv)
{
// Initialize libMesh and any dependent libaries, like in example 2.
LibMeshInit init (argc, argv);
// Only our PETSc interface currently supports solves restricted to
// subdomains
libmesh_example_requires(libMesh::default_solver_package() == PETSC_SOLVERS, "--enable-petsc");
// Skip adaptive examples on a non-adaptive libMesh build
#ifndef LIBMESH_ENABLE_AMR
libmesh_example_requires(false, "--enable-amr");
#else
// 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.
// 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 = "FIRST";
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"))
libmesh_error_msg("This example requires a C^0 (or higher) FE basis.");
// Create a mesh, with dimension to be overridden later, on the
// default MPI communicator.
Mesh mesh(init.comm());
// 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));
}
// To demonstate solving on a subdomain, we will solve only on the
// interior of a circle (ball in 3d) with radius 0.8. So show that
// this also works well on locally refined meshes, we refine once
// all elements that are located on the boundary of this circle (or
// ball).
{
// A MeshRefinement object is needed to refine meshes.
MeshRefinement meshRefinement(mesh);
// Loop over all elements.
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->active())
{
// Just check whether the current element has at least one
// node inside and one node outside the circle.
bool node_in = false;
bool node_out = false;
for (unsigned int i=0; i<elem->n_nodes(); i++)
{
double d = elem->point(i).norm();
if (d<0.8)
{
node_in = true;
}
else
{
node_out = true;
}
}
if (node_in && node_out)
{
elem->set_refinement_flag(Elem::REFINE);
}
else
{
elem->set_refinement_flag(Elem::DO_NOTHING);
}
}
else
{
elem->set_refinement_flag(Elem::INACTIVE);
}
}
// Now actually refine.
meshRefinement.refine_elements();
}
// Print information about the mesh to the screen.
mesh.print_info();
// Now set the subdomain_id of all elements whose centroid is inside
// the circle to 1.
{
// Loop over all elements.
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;
double d = elem->centroid().norm();
if (d<0.8)
{
elem->subdomain_id() = 1;
}
}
}
// 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");
// Add the variable "u" to "Poisson". "u"
// will be approximated using second-order approximation.
system.add_variable("u",
Utility::string_to_enum<Order> (order),
Utility::string_to_enum<FEFamily>(family));
// 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();
// Restrict solves to those elements that have subdomain_id set to 1.
std::set<subdomain_id_type> id_list;
id_list.insert(1);
SystemSubsetBySubdomain::SubdomainSelectionByList selection(id_list);
SystemSubsetBySubdomain subset(system, selection);
system.restrict_solve_to(&subset, SUBSET_ZERO);
// Note that using SUBSET_ZERO will cause all dofs outside the
// subdomain to be cleared. This will, however, cause some hanging
// nodes outside the subdomain to have inconsistent values.
// 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 1, 1D", GnuPlotIO::GRID_ON);
plot.write_equation_systems("gnuplot_script", equation_systems);
}
else
{
GMVIO (mesh).write_equation_systems ((dim == 3) ?
"out_3.gmv" : "out_2.gmv", equation_systems);
#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
}
#endif // #ifndef LIBMESH_ENABLE_AMR
// All done.
return 0;
}
bool MeshRefinement::flag_elements_by_nelem_target (const ErrorVector& error_per_cell)
{
parallel_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 unsigned int n_active_elem = _mesh.n_active_elem();
// The maximum number of active elements to flag for coarsening
const unsigned int max_elem_coarsen =
static_cast<unsigned int>(_coarsen_fraction * n_active_elem) + 1;
// The maximum number of elements to flag for refinement
const unsigned int max_elem_refine =
static_cast<unsigned int>(_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 int n_elem_new = _nelem_target - n_active_elem;
// Create an vector with active element errors and ids,
// sorted by highest errors first
const unsigned int max_elem_id = _mesh.max_elem_id();
std::vector<std::pair<float, unsigned int> > 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 unsigned int 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));
}
CommWorld.max(is_active);
CommWorld.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<float, unsigned int> > 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 (unsigned int 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
unsigned int coarsen_count = 0;
unsigned int 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(static_cast<unsigned int>(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(static_cast<unsigned int>(-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
unsigned int successful_refine_count = 0;
{
std::vector<bool> is_refinable(max_elem_id, false);
for (unsigned int i=0; i != sorted_error.size(); ++i)
{
unsigned int eid = sorted_error[i].second;
Elem *elem = _mesh.query_elem(eid);
if (elem && elem->level() < _max_h_level)
is_refinable[eid] = true;
}
CommWorld.max(is_refinable);
if (refine_count > max_elem_refine)
refine_count = max_elem_refine;
for (unsigned int i=0; i != sorted_error.size(); ++i)
{
if (successful_refine_count >= refine_count)
break;
unsigned int 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;
unsigned int successful_coarsen_count = 0;
if (coarsen_count)
{
for (unsigned int i=0; i != sorted_parent_error.size(); ++i)
{
if (successful_coarsen_count >= coarsen_count * twotodim)
break;
unsigned int 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;
}
bool UnstructuredMesh::contract ()
{
LOG_SCOPE ("contract()", "Mesh");
// Flag indicating if this call actually changes the mesh
bool mesh_changed = false;
element_iterator in = elements_begin();
const element_iterator end = elements_end();
#ifdef DEBUG
for ( ; in != end; ++in)
if (*in != libmesh_nullptr)
{
Elem * el = *in;
libmesh_assert(el->active() || el->subactive() || el->ancestor());
}
in = elements_begin();
#endif
// Loop over the elements.
for ( ; in != end; ++in)
if (*in != libmesh_nullptr)
{
Elem * el = *in;
// Delete all the subactive ones
if (el->subactive())
{
// No level-0 element should be subactive.
// Note that we CAN'T test elem->level(), as that
// touches elem->parent()->dim(), and elem->parent()
// might have already been deleted!
libmesh_assert(el->parent());
// Delete the element
// This just sets a pointer to NULL, and doesn't
// invalidate any iterators
this->delete_elem(el);
// the mesh has certainly changed
mesh_changed = true;
}
else
{
// Compress all the active ones
if (el->active())
el->contract();
else
libmesh_assert (el->ancestor());
}
}
// Strip any newly-created NULL voids out of the element array
this->renumber_nodes_and_elements();
// FIXME: Need to understand why deleting subactive children
// invalidates the point locator. For now we will clear it explicitly
this->clear_point_locator();
return mesh_changed;
}
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 unpack(std::vector<largest_id_type>::const_iterator in,
Elem** out,
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 =
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_greater_equal (rflag, 0);
libmesh_assert_less (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_greater_equal (pflag, 0);
libmesh_assert_less (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_greater_equal (typeint, 0);
libmesh_assert_less (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 processor_id_type processor_id =
static_cast<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 =
static_cast<subdomain_id_type>(*in++);
// int 7: dof object id
const dof_id_type id =
static_cast<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 =
static_cast<unique_id_type>(*in++);
#endif
#ifdef LIBMESH_ENABLE_AMR
// int 9: parent dof object id
const dof_id_type parent_id =
static_cast<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
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_equal_to (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_equal_to (elem->level(), level);
libmesh_assert_equal_to (elem->id(), id);
//#ifdef LIBMESH_ENABLE_UNIQUE_ID
// No check for unqiue 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(i) ==
static_cast<dof_id_type>(*in++));
#else
in += n_nodes;
#endif
#ifdef LIBMESH_ENABLE_AMR
libmesh_assert_equal_to (elem->p_level(), p_level);
libmesh_assert_equal_to (elem->refinement_flag(), refinement_flag);
libmesh_assert_equal_to (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 dof_id_type neighbor_id =
static_cast<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(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(n));
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_equal_to (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_equal_to (parent_id, static_cast<dof_id_type>(-1));
#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(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 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;
#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
(static_cast<dof_id_type>(*in++));
for (unsigned int n=0; n<elem->n_neighbors(); n++)
{
const dof_id_type neighbor_id =
static_cast<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(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_greater_equal (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;
}
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;
}
// Begin the main program. Note that the first
// statement in the program throws an error if
// you are in complex number mode, since this
// example is only intended to work with real
// numbers.
int main (int argc, char ** argv)
{
// Initialize libMesh.
LibMeshInit init (argc, argv);
#if !defined(LIBMESH_ENABLE_AMR)
libmesh_example_requires(false, "--enable-amr");
#else
libmesh_example_requires(libMesh::default_solver_package() == PETSC_SOLVERS, "--enable-petsc");
// Brief message to the user regarding the program name
// and command line arguments.
libMesh::out << "Running: " << argv[0];
for (int i=1; i<argc; i++)
libMesh::out << " " << argv[i];
libMesh::out << std::endl << std::endl;
// Skip this 2D example if libMesh was compiled as 1D-only.
libmesh_example_requires(2 <= LIBMESH_DIM, "2D support");
// Create a mesh, with dimension to be overridden later, distributed
// across the default MPI communicator.
Mesh mesh(init.comm());
// Create an equation systems object.
EquationSystems equation_systems (mesh);
MeshTools::Generation::build_square (mesh,
16,
16,
-1., 1.,
-1., 1.,
QUAD4);
LinearImplicitSystem & system =
equation_systems.add_system<LinearImplicitSystem>
("System");
// Adds the variable "u" to "System". "u"
// will be approximated using first-order approximation.
system.add_variable ("u", FIRST);
// Also, we need to add two vectors. The tensor matrix v*w^T of
// these two vectors will be part of the system matrix.
system.add_vector("v", false);
system.add_vector("w", false);
// We need an additional matrix to be used for preconditioning since
// a shell matrix is not suitable for that.
system.add_matrix("Preconditioner");
// Give the system a pointer to the matrix assembly function.
system.attach_assemble_function (assemble);
// Initialize the data structures for the equation system.
equation_systems.init ();
// Prints information about the system to the screen.
equation_systems.print_info();
equation_systems.parameters.set<unsigned int>
("linear solver maximum iterations") = 250;
equation_systems.parameters.set<Real>
("linear solver tolerance") = TOLERANCE;
// Refine arbitrarily some elements.
for (unsigned int i=0; i<2; i++)
{
MeshRefinement mesh_refinement(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->active())
{
if ((elem->id()%20)>8)
{
elem->set_refinement_flag(Elem::REFINE);
}
else
{
elem->set_refinement_flag(Elem::DO_NOTHING);
}
}
else
{
elem->set_refinement_flag(Elem::INACTIVE);
}
}
mesh_refinement.refine_elements();
equation_systems.reinit();
}
// Prints information about the system to the screen.
equation_systems.print_info();
// Before the assemblation of the matrix, we have to clear the two
// vectors that form the tensor matrix (since this is not performed
// automatically).
system.get_vector("v").init(system.n_dofs(), system.n_local_dofs());
system.get_vector("w").init(system.n_dofs(), system.n_local_dofs());
// We need a shell matrix to solve. There is currently no way to
// store the shell matrix in the system. We just create it locally
// here (a shell matrix does not occupy much memory).
SumShellMatrix<Number> shellMatrix(system.comm());
TensorShellMatrix<Number> shellMatrix0(system.get_vector("v"), system.get_vector("w"));
shellMatrix.matrices.push_back(&shellMatrix0);
SparseShellMatrix<Number> shellMatrix1(*system.matrix);
shellMatrix.matrices.push_back(&shellMatrix1);
// Attach that to the system.
system.attach_shell_matrix(&shellMatrix);
// Reset the preconditioning matrix to zero (for the system matrix,
// the same thing is done automatically).
system.get_matrix("Preconditioner").zero();
// Assemble & solve the linear system
system.solve();
// Detach the shell matrix from the system since it will go out of
// scope. Nobody should solve the system outside this function.
system.detach_shell_matrix();
// Print a nice message.
libMesh::out << "Solved linear system in "
<< system.n_linear_iterations()
<< " iterations, residual norm is "
<< system.final_linear_residual()
<< "."
<< std::endl;
#if defined(LIBMESH_HAVE_VTK) && !defined(LIBMESH_ENABLE_PARMESH)
// Write result to file.
VTKIO(mesh).write_equation_systems ("out.pvtu", equation_systems);
#endif // #ifdef LIBMESH_HAVE_VTK
#endif // #ifndef LIBMESH_ENABLE_AMR
return 0;
}