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 HPSingularity::select_refinement (System &system)
{
START_LOG("select_refinement()", "HPSingularity");
// The current mesh
MeshBase& mesh = system.get_mesh();
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)
{
Elem* elem = *elem_it;
// We're only checking elements that are already flagged for h
// refinement
if (elem->refinement_flag() != Elem::REFINE)
continue;
elem->set_p_refinement_flag(Elem::REFINE);
elem->set_refinement_flag(Elem::DO_NOTHING);
for (std::list<Point>::iterator ppoint =
singular_points.begin();
ppoint != singular_points.end(); ++ppoint)
{
if (elem->contains_point(*ppoint))
{
elem->set_p_refinement_flag(Elem::DO_NOTHING);
elem->set_refinement_flag(Elem::REFINE);
break;
}
}
}
STOP_LOG("select_refinement()", "HPSingularity");
}
void MeshRefinement::flag_elements_by_elem_fraction (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
parallel_only();
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// The number of active elements in the mesh
const unsigned int n_active_elem = _mesh.n_elem();
// The number of elements to flag for coarsening
const unsigned int n_elem_coarsen =
static_cast<unsigned int>(_coarsen_fraction * n_active_elem);
// The number of elements to flag for refinement
const unsigned int n_elem_refine =
static_cast<unsigned int>(_refine_fraction * n_active_elem);
// Clean up the refinement flags. These could be left
// over from previous refinement steps.
this->clean_refinement_flags();
// This vector stores the error and element number for all the
// active elements. It will be sorted and the top & bottom
// elements will then be flagged for coarsening & refinement
std::vector<float> sorted_error;
sorted_error.reserve (n_active_elem);
// Loop over the active elements and create the entry
// in the sorted_error vector
MeshBase::element_iterator elem_it = _mesh.active_local_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_local_elements_end();
for (; elem_it != elem_end; ++elem_it)
sorted_error.push_back (error_per_cell[(*elem_it)->id()]);
CommWorld.allgather(sorted_error);
// Now sort the sorted_error vector
std::sort (sorted_error.begin(), sorted_error.end());
// If we're coarsening by parents:
// Create a sorted error vector with coarsenable parent elements
// only, sorted by lowest errors first
ErrorVector error_per_parent, sorted_parent_error;
if (_coarsen_by_parents)
{
Real parent_error_min, parent_error_max;
create_parent_error_vector(error_per_cell,
error_per_parent,
parent_error_min,
parent_error_max);
sorted_parent_error = error_per_parent;
std::sort (sorted_parent_error.begin(), sorted_parent_error.end());
// All the other error values will be 0., so get rid of them.
sorted_parent_error.erase (std::remove(sorted_parent_error.begin(),
sorted_parent_error.end(), 0.),
sorted_parent_error.end());
}
float top_error= 0., bottom_error = 0.;
// Get the maximum error value corresponding to the
// bottom n_elem_coarsen elements
if (_coarsen_by_parents && n_elem_coarsen)
{
const unsigned int dim = _mesh.mesh_dimension();
unsigned int twotodim = 1;
for (unsigned int i=0; i!=dim; ++i)
twotodim *= 2;
unsigned int n_parent_coarsen = n_elem_coarsen / (twotodim - 1);
if (n_parent_coarsen)
bottom_error = sorted_parent_error[n_parent_coarsen - 1];
}
else if (n_elem_coarsen)
{
bottom_error = sorted_error[n_elem_coarsen - 1];
}
if (n_elem_refine)
top_error = sorted_error[sorted_error.size() - n_elem_refine];
// Finally, let's do the element flagging
elem_it = _mesh.active_elements_begin();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
Elem* parent = elem->parent();
if (_coarsen_by_parents && parent && n_elem_coarsen &&
error_per_parent[parent->id()] <= bottom_error)
elem->set_refinement_flag(Elem::COARSEN);
if (!_coarsen_by_parents && n_elem_coarsen &&
error_per_cell[elem->id()] <= bottom_error)
elem->set_refinement_flag(Elem::COARSEN);
if (n_elem_refine &&
elem->level() < _max_h_level &&
error_per_cell[elem->id()] >= top_error)
elem->set_refinement_flag(Elem::REFINE);
}
}
//-----------------------------------------------------------------
// Mesh refinement methods
void MeshRefinement::flag_elements_by_error_fraction (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
parallel_only();
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// Clean up the refinement flags. These could be left
// over from previous refinement steps.
this->clean_refinement_flags();
// We're getting the minimum and maximum error values
// for the ACTIVE elements
Real error_min = 1.e30;
Real error_max = 0.;
// And, if necessary, for their parents
Real parent_error_min = 1.e30;
Real parent_error_max = 0.;
// Prepare another error vector if we need to sum parent errors
ErrorVector error_per_parent;
if (_coarsen_by_parents)
{
create_parent_error_vector(error_per_cell,
error_per_parent,
parent_error_min,
parent_error_max);
}
// We need to loop over all active elements to find the minimum
MeshBase::element_iterator el_it =
_mesh.active_local_elements_begin();
const MeshBase::element_iterator el_end =
_mesh.active_local_elements_end();
for (; el_it != el_end; ++el_it)
{
const unsigned int id = (*el_it)->id();
libmesh_assert_less (id, error_per_cell.size());
error_max = std::max (error_max, error_per_cell[id]);
error_min = std::min (error_min, error_per_cell[id]);
}
CommWorld.max(error_max);
CommWorld.min(error_min);
// Compute the cutoff values for coarsening and refinement
const Real error_delta = (error_max - error_min);
const Real parent_error_delta = parent_error_max - parent_error_min;
const Real refine_cutoff = (1.- _refine_fraction)*error_max;
const Real coarsen_cutoff = _coarsen_fraction*error_delta + error_min;
const Real parent_cutoff = _coarsen_fraction*parent_error_delta + error_min;
// // Print information about the error
// libMesh::out << " Error Information:" << std::endl
// << " ------------------" << std::endl
// << " min: " << error_min << std::endl
// << " max: " << error_max << std::endl
// << " delta: " << error_delta << std::endl
// << " refine_cutoff: " << refine_cutoff << std::endl
// << " coarsen_cutoff: " << coarsen_cutoff << std::endl;
// Loop over the elements and flag them for coarsening or
// refinement based on the element error
MeshBase::element_iterator e_it =
_mesh.active_elements_begin();
const MeshBase::element_iterator e_end =
_mesh.active_elements_end();
for (; e_it != e_end; ++e_it)
{
Elem* elem = *e_it;
const unsigned int id = elem->id();
libmesh_assert_less (id, error_per_cell.size());
const float elem_error = error_per_cell[id];
if (_coarsen_by_parents)
{
Elem* parent = elem->parent();
if (parent)
{
const unsigned int parentid = parent->id();
if (error_per_parent[parentid] >= 0. &&
error_per_parent[parentid] <= parent_cutoff)
elem->set_refinement_flag(Elem::COARSEN);
}
}
// Flag the element for coarsening if its error
// is <= coarsen_fraction*delta + error_min
else if (elem_error <= coarsen_cutoff)
{
elem->set_refinement_flag(Elem::COARSEN);
}
// Flag the element for refinement if its error
// is >= refinement_cutoff.
if (elem_error >= refine_cutoff)
if (elem->level() < _max_h_level)
elem->set_refinement_flag(Elem::REFINE);
}
}
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;
}
void MeshRefinement::flag_elements_by_error_tolerance (const ErrorVector& error_per_cell_in)
{
parallel_only();
libmesh_assert_greater (_coarsen_threshold, 0);
// Check for valid fractions..
// The fraction values must be in [0,1]
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// How much error per cell will we tolerate?
const Real local_refinement_tolerance =
_absolute_global_tolerance / std::sqrt(static_cast<Real>(_mesh.n_active_elem()));
const Real local_coarsening_tolerance =
local_refinement_tolerance * _coarsen_threshold;
// Prepare another error vector if we need to sum parent errors
ErrorVector error_per_parent;
if (_coarsen_by_parents)
{
Real parent_error_min, parent_error_max;
create_parent_error_vector(error_per_cell_in,
error_per_parent,
parent_error_min,
parent_error_max);
}
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
Elem* parent = elem->parent();
const unsigned int elem_number = elem->id();
const float elem_error = error_per_cell_in[elem_number];
if (elem_error > local_refinement_tolerance &&
elem->level() < _max_h_level)
elem->set_refinement_flag(Elem::REFINE);
if (!_coarsen_by_parents && elem_error <
local_coarsening_tolerance)
elem->set_refinement_flag(Elem::COARSEN);
if (_coarsen_by_parents && parent)
{
float parent_error = error_per_parent[parent->id()];
if (parent_error >= 0.)
{
const Real parent_coarsening_tolerance =
std::sqrt(parent->n_children() *
local_coarsening_tolerance *
local_coarsening_tolerance);
if (parent_error < parent_coarsening_tolerance)
elem->set_refinement_flag(Elem::COARSEN);
}
}
}
}
void UnstructuredMesh::copy_nodes_and_elements(const UnstructuredMesh & other_mesh,
const bool skip_find_neighbors)
{
// We're assuming our subclass data needs no copy
libmesh_assert_equal_to (_n_parts, other_mesh._n_parts);
libmesh_assert (std::equal(_elem_dims.begin(), _elem_dims.end(), other_mesh._elem_dims.begin()));
libmesh_assert_equal_to (_is_prepared, other_mesh._is_prepared);
// We're assuming the other mesh has proper element number ordering,
// so that we add parents before their children.
#ifdef DEBUG
MeshTools::libmesh_assert_valid_amr_elem_ids(other_mesh);
#endif
//Copy in Nodes
{
//Preallocate Memory if necessary
this->reserve_nodes(other_mesh.n_nodes());
const_node_iterator it = other_mesh.nodes_begin();
const_node_iterator end = other_mesh.nodes_end();
for (; it != end; ++it)
{
const Node * oldn = *it;
// Add new nodes in old node Point locations
#ifdef LIBMESH_ENABLE_UNIQUE_ID
Node *newn =
#endif
this->add_point(*oldn, oldn->id(), oldn->processor_id());
#ifdef LIBMESH_ENABLE_UNIQUE_ID
newn->set_unique_id() = oldn->unique_id();
#endif
}
}
//Copy in Elements
{
//Preallocate Memory if necessary
this->reserve_elem(other_mesh.n_elem());
// Declare a map linking old and new elements, needed to copy the neighbor lists
std::map<const Elem *, Elem *> old_elems_to_new_elems;
// Loop over the elements
MeshBase::const_element_iterator it = other_mesh.elements_begin();
const MeshBase::const_element_iterator end = other_mesh.elements_end();
// FIXME: Where do we set element IDs??
for (; it != end; ++it)
{
//Look at the old element
const Elem * old = *it;
//Build a new element
Elem * newparent = old->parent() ?
this->elem_ptr(old->parent()->id()) : libmesh_nullptr;
UniquePtr<Elem> ap = Elem::build(old->type(), newparent);
Elem * el = ap.release();
el->subdomain_id() = old->subdomain_id();
for (unsigned int s=0; s != old->n_sides(); ++s)
if (old->neighbor_ptr(s) == remote_elem)
el->set_neighbor(s, const_cast<RemoteElem *>(remote_elem));
#ifdef LIBMESH_ENABLE_AMR
if (old->has_children())
for (unsigned int c=0; c != old->n_children(); ++c)
if (old->child_ptr(c) == remote_elem)
el->add_child(const_cast<RemoteElem *>(remote_elem), c);
//Create the parent's child pointers if necessary
if (newparent)
{
unsigned int oldc = old->parent()->which_child_am_i(old);
newparent->add_child(el, oldc);
}
// Copy the refinement flags
el->set_refinement_flag(old->refinement_flag());
// Use hack_p_level since we may not have sibling elements
// added yet
el->hack_p_level(old->p_level());
el->set_p_refinement_flag(old->p_refinement_flag());
#endif // #ifdef LIBMESH_ENABLE_AMR
//Assign all the nodes
for(unsigned int i=0;i<el->n_nodes();i++)
el->set_node(i) = this->node_ptr(old->node_id(i));
// And start it off in the same subdomain
el->processor_id() = old->processor_id();
// Give it the same ids
el->set_id(old->id());
#ifdef LIBMESH_ENABLE_UNIQUE_ID
el->set_unique_id() = old->unique_id();
#endif
//Hold onto it
if(!skip_find_neighbors)
{
this->add_elem(el);
}
else
{
Elem * new_el = this->add_elem(el);
old_elems_to_new_elems[old] = new_el;
}
// Add the link between the original element and this copy to the map
if(skip_find_neighbors)
old_elems_to_new_elems[old] = el;
}
// Loop (again) over the elements to fill in the neighbors
if(skip_find_neighbors)
{
it = other_mesh.elements_begin();
for (; it != end; ++it)
{
Elem * old_elem = *it;
Elem * new_elem = old_elems_to_new_elems[old_elem];
for (unsigned int s=0; s != old_elem->n_neighbors(); ++s)
{
const Elem * old_neighbor = old_elem->neighbor_ptr(s);
Elem * new_neighbor = old_elems_to_new_elems[old_neighbor];
new_elem->set_neighbor(s, new_neighbor);
}
}
}
}
//Finally prepare the new Mesh for use. Keep the same numbering and
//partitioning but also the same renumbering and partitioning
//policies as our source mesh.
this->allow_renumbering(false);
this->skip_partitioning(true);
this->prepare_for_use(false, skip_find_neighbors);
this->allow_renumbering(other_mesh.allow_renumbering());
this->skip_partitioning(other_mesh.skip_partitioning());
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_node (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_object_only();
bool flags_changed = false;
// Vector holding the maximum element level that touches a node.
std::vector<unsigned char> max_level_at_node (_mesh.n_nodes(), 0);
std::vector<unsigned char> max_p_level_at_node (_mesh.n_nodes(), 0);
// Loop over all the active elements & fill the vector
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem* elem = *elem_it;
const unsigned char elem_level =
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));
// Set the max_level at each node
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const dof_id_type node_number = elem->node(n);
libmesh_assert_less (node_number, max_level_at_node.size());
max_level_at_node[node_number] =
std::max (max_level_at_node[node_number], elem_level);
max_p_level_at_node[node_number] =
std::max (max_p_level_at_node[node_number], elem_p_level);
}
}
}
// Now loop over the active elements and flag the elements
// who violate the requested level mismatch. Alternatively, if
// _enforce_mismatch_limit_prior_to_refinement is true, swap refinement flags
// accordingly.
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
const unsigned int elem_level = elem->level();
const unsigned int elem_p_level = elem->p_level();
// Skip the element if it is already fully flagged
// unless we are enforcing mismatch prior to refienemnt and may need to
// remove the refinement flag(s)
if (elem->refinement_flag() == Elem::REFINE &&
elem->p_refinement_flag() == Elem::REFINE
&& !_enforce_mismatch_limit_prior_to_refinement)
continue;
// Loop over the nodes, check for possible mismatch
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const dof_id_type node_number = elem->node(n);
// Flag the element for refinement if it violates
// the requested level mismatch
if ((elem_level + max_mismatch) < max_level_at_node[node_number]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ((elem_p_level + max_mismatch) < max_p_level_at_node[node_number]
&& elem->p_refinement_flag() != Elem::REFINE)
{
elem->set_p_refinement_flag (Elem::REFINE);
flags_changed = true;
}
// Possibly enforce limit mismatch prior to refinement
flags_changed |= this->enforce_mismatch_limit_prior_to_refinement(elem, POINT, max_mismatch);
}
}
}
// If flags changed on any processor then they changed globally
this->comm().max(flags_changed);
return flags_changed;
}
void Elem::coarsen()
{
libmesh_assert (this->refinement_flag() == Elem::COARSEN_INACTIVE);
libmesh_assert (!this->active());
// We no longer delete children until MeshRefinement::contract()
// delete [] _children;
// _children = NULL;
unsigned int parent_p_level = 0;
// re-compute hanging node nodal locations
for (unsigned int c=0; c<this->n_children(); c++)
{
Elem *mychild = this->child(c);
if (mychild == remote_elem)
continue;
for (unsigned int nc=0; nc<mychild->n_nodes(); nc++)
{
Point new_pos;
bool calculated_new_pos = false;
for (unsigned int n=0; n<this->n_nodes(); n++)
{
// The value from the embedding matrix
const float em_val = this->embedding_matrix(c,nc,n);
// The node location is somewhere between existing vertices
if ((em_val != 0.) && (em_val != 1.))
{
new_pos.add_scaled (this->point(n), em_val);
calculated_new_pos = true;
}
}
if(calculated_new_pos)
{
//Move the existing node back into it's original location
for(unsigned int i=0; i<LIBMESH_DIM; i++)
{
Point & child_node = *(mychild->get_node(nc));
child_node(i)=new_pos(i);
}
}
}
}
for (unsigned int c=0; c<this->n_children(); c++)
{
Elem *mychild = this->child(c);
if (mychild == remote_elem)
continue;
libmesh_assert (mychild->refinement_flag() == Elem::COARSEN);
mychild->set_refinement_flag(Elem::INACTIVE);
if (mychild->p_level() > parent_p_level)
parent_p_level = mychild->p_level();
}
this->set_refinement_flag(Elem::JUST_COARSENED);
this->set_p_level(parent_p_level);
libmesh_assert (this->active());
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_node (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
// Vector holding the maximum element level that touches a node.
std::vector<unsigned char> max_level_at_node (_mesh.n_nodes(), 0);
std::vector<unsigned char> max_p_level_at_node (_mesh.n_nodes(), 0);
// Loop over all the active elements & fill the vector
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem* elem = *elem_it;
const unsigned char elem_level =
elem->level() + ((elem->refinement_flag() == Elem::REFINE) ? 1 : 0);
const unsigned char elem_p_level =
elem->p_level() + ((elem->p_refinement_flag() == Elem::REFINE) ? 1 : 0);
// Set the max_level at each node
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const unsigned int node_number = elem->node(n);
libmesh_assert_less (node_number, max_level_at_node.size());
max_level_at_node[node_number] =
std::max (max_level_at_node[node_number], elem_level);
max_p_level_at_node[node_number] =
std::max (max_p_level_at_node[node_number], elem_p_level);
}
}
}
// Now loop over the active elements and flag the elements
// who violate the requested level mismatch
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
const unsigned int elem_level = elem->level();
const unsigned int elem_p_level = elem->p_level();
// Skip the element if it is already fully flagged
if (elem->refinement_flag() == Elem::REFINE &&
elem->p_refinement_flag() == Elem::REFINE)
continue;
// Loop over the nodes, check for possible mismatch
for (unsigned int n=0; n<elem->n_nodes(); n++)
{
const unsigned int node_number = elem->node(n);
// Flag the element for refinement if it violates
// the requested level mismatch
if ( (elem_level + max_mismatch) < max_level_at_node[node_number]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ( (elem_p_level + max_mismatch) < max_p_level_at_node[node_number]
&& elem->p_refinement_flag() != Elem::REFINE)
{
elem->set_p_refinement_flag (Elem::REFINE);
flags_changed = true;
}
}
}
}
// If flags changed on any processor then they changed globally
CommWorld.max(flags_changed);
return flags_changed;
}
bool MeshRefinement::eliminate_unrefined_patches ()
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
// First assume that we'll have to flag this element for both h
// and p refinement, then change our minds if we see any
// neighbors that are as coarse or coarser than us.
bool h_flag_me = true,
p_flag_me = true;
// Skip the element if it is already fully flagged for refinement
if (elem->p_refinement_flag() == Elem::REFINE)
p_flag_me = false;
if (elem->refinement_flag() == Elem::REFINE)
{
h_flag_me = false;
if (!p_flag_me)
continue;
}
// Test the parent if that is already flagged for coarsening
else if (elem->refinement_flag() == Elem::COARSEN)
{
libmesh_assert(elem->parent());
elem = elem->parent();
// FIXME - this doesn't seem right - RHS
if (elem->refinement_flag() != Elem::COARSEN_INACTIVE)
continue;
p_flag_me = false;
}
const unsigned int my_level = elem->level();
int my_p_adjustment = 0;
if (elem->p_refinement_flag() == Elem::REFINE)
my_p_adjustment = 1;
else if (elem->p_refinement_flag() == Elem::COARSEN)
{
libmesh_assert_greater (elem->p_level(), 0);
my_p_adjustment = -1;
}
const unsigned int my_new_p_level = elem->p_level() +
my_p_adjustment;
// Check all the element neighbors
for (unsigned int n=0; n<elem->n_neighbors(); n++)
{
const Elem *neighbor = elem->neighbor(n);
// Quit if the element is on a local boundary
if (neighbor == NULL || neighbor == remote_elem)
{
h_flag_me = false;
p_flag_me = false;
break;
}
// if the neighbor will be equally or less refined than
// we are, then we will not become an unrefined island.
// So if we are still considering h refinement:
if (h_flag_me &&
// If our neighbor is already at a lower level,
// it can't end up at a higher level even if it
// is flagged for refinement once
((neighbor->level() < my_level) ||
// If our neighbor is at the same level but isn't
// flagged for refinement, it won't end up at a
// higher level
((neighbor->active()) &&
(neighbor->refinement_flag() != Elem::REFINE)) ||
// If our neighbor is currently more refined but is
// a parent flagged for coarsening, it will end up
// at the same level.
(neighbor->refinement_flag() == Elem::COARSEN_INACTIVE)))
{
// We've proven we won't become an unrefined island,
// so don't h refine to avoid that.
h_flag_me = false;
// If we've also proven we don't need to p refine,
// we don't need to check more neighbors
if (!p_flag_me)
break;
}
if (p_flag_me)
{
// if active neighbors will have a p level
// equal to or lower than ours, then we do not need to p
// refine ourselves.
if (neighbor->active())
{
int p_adjustment = 0;
if (neighbor->p_refinement_flag() == Elem::REFINE)
p_adjustment = 1;
else if (neighbor->p_refinement_flag() == Elem::COARSEN)
{
libmesh_assert_greater (neighbor->p_level(), 0);
p_adjustment = -1;
}
if (my_new_p_level >= neighbor->p_level() + p_adjustment)
{
p_flag_me = false;
if (!h_flag_me)
break;
}
}
// If we have inactive neighbors, we need to
// test all their active descendants which neighbor us
else if (neighbor->ancestor())
{
if (neighbor->min_new_p_level_by_neighbor(elem,
my_new_p_level + 2) <= my_new_p_level)
{
p_flag_me = false;
if (!h_flag_me)
break;
}
}
}
}
if (h_flag_me)
{
// Parents that would create islands should no longer
// coarsen
if (elem->refinement_flag() == Elem::COARSEN_INACTIVE)
{
for (unsigned int c=0; c<elem->n_children(); c++)
{
libmesh_assert_equal_to (elem->child(c)->refinement_flag(),
Elem::COARSEN);
elem->child(c)->set_refinement_flag(Elem::DO_NOTHING);
}
elem->set_refinement_flag(Elem::INACTIVE);
}
else
elem->set_refinement_flag(Elem::REFINE);
flags_changed = true;
}
if (p_flag_me)
{
if (elem->p_refinement_flag() == Elem::COARSEN)
elem->set_p_refinement_flag(Elem::DO_NOTHING);
else
elem->set_p_refinement_flag(Elem::REFINE);
flags_changed = true;
}
}
// If flags changed on any processor then they changed globally
CommWorld.max(flags_changed);
return flags_changed;
}
//-----------------------------------------------------------------
// Mesh refinement methods
bool MeshRefinement::limit_level_mismatch_at_edge (const unsigned int max_mismatch)
{
// This function must be run on all processors at once
parallel_only();
bool flags_changed = false;
// Maps holding the maximum element level that touches an edge
std::map<std::pair<unsigned int, unsigned int>, unsigned char>
max_level_at_edge;
std::map<std::pair<unsigned int, unsigned int>, unsigned char>
max_p_level_at_edge;
// Loop over all the active elements & fill the maps
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem* elem = *elem_it;
const unsigned char elem_level =
elem->level() + ((elem->refinement_flag() == Elem::REFINE) ? 1 : 0);
const unsigned char elem_p_level =
elem->p_level() + ((elem->p_refinement_flag() == Elem::REFINE) ? 1 : 0);
// Set the max_level at each edge
for (unsigned int n=0; n<elem->n_edges(); n++)
{
AutoPtr<Elem> edge = elem->build_edge(n);
unsigned int childnode0 = edge->node(0);
unsigned int childnode1 = edge->node(1);
if (childnode1 < childnode0)
std::swap(childnode0, childnode1);
for (const Elem *p = elem; p != NULL; p = p->parent())
{
AutoPtr<Elem> pedge = p->build_edge(n);
unsigned int node0 = pedge->node(0);
unsigned int node1 = pedge->node(1);
if (node1 < node0)
std::swap(node0, node1);
// If elem does not share this edge with its ancestor
// p, refinement levels of elements sharing p's edge
// are not restricted by refinement levels of elem.
// Furthermore, elem will not share this edge with any
// of p's ancestors, so we can safely break out of the
// for loop early.
if (node0 != childnode0 && node1 != childnode1)
break;
childnode0 = node0;
childnode1 = node1;
std::pair<unsigned int, unsigned int> edge_key =
std::make_pair(node0, node1);
if (max_level_at_edge.find(edge_key) ==
max_level_at_edge.end())
{
max_level_at_edge[edge_key] = elem_level;
max_p_level_at_edge[edge_key] = elem_p_level;
}
else
{
max_level_at_edge[edge_key] =
std::max (max_level_at_edge[edge_key], elem_level);
max_p_level_at_edge[edge_key] =
std::max (max_p_level_at_edge[edge_key], elem_p_level);
}
}
}
}
}
// Now loop over the active elements and flag the elements
// who violate the requested level mismatch
{
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
const unsigned int elem_level = elem->level();
const unsigned int elem_p_level = elem->p_level();
// Skip the element if it is already fully flagged
if (elem->refinement_flag() == Elem::REFINE &&
elem->p_refinement_flag() == Elem::REFINE)
continue;
// Loop over the nodes, check for possible mismatch
for (unsigned int n=0; n<elem->n_edges(); n++)
{
AutoPtr<Elem> edge = elem->build_edge(n);
unsigned int node0 = edge->node(0);
unsigned int node1 = edge->node(1);
if (node1 < node0)
std::swap(node0, node1);
std::pair<unsigned int, unsigned int> edge_key =
std::make_pair(node0, node1);
// Flag the element for refinement if it violates
// the requested level mismatch
if ( (elem_level + max_mismatch) < max_level_at_edge[edge_key]
&& elem->refinement_flag() != Elem::REFINE)
{
elem->set_refinement_flag (Elem::REFINE);
flags_changed = true;
}
if ( (elem_p_level + max_mismatch) < max_p_level_at_edge[edge_key]
&& elem->p_refinement_flag() != Elem::REFINE)
{
elem->set_p_refinement_flag (Elem::REFINE);
flags_changed = true;
}
}
}
}
// If flags changed on any processor then they changed globally
CommWorld.max(flags_changed);
return flags_changed;
}
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;
}
void HPCoarsenTest::select_refinement (System & system)
{
START_LOG("select_refinement()", "HPCoarsenTest");
// The current mesh
MeshBase & mesh = system.get_mesh();
// The dimensionality of the mesh
const unsigned int dim = mesh.mesh_dimension();
// The number of variables in the system
const unsigned int n_vars = system.n_vars();
// The DofMap for this system
const DofMap & dof_map = system.get_dof_map();
// The system number (for doing bad hackery)
const unsigned int sys_num = system.number();
// Check for a valid component_scale
if (!component_scale.empty())
{
if (component_scale.size() != n_vars)
libmesh_error_msg("ERROR: component_scale is the wrong size:\n" \
<< " component_scale.size()=" \
<< component_scale.size() \
<< "\n n_vars=" \
<< n_vars);
}
else
{
// No specified scaling. Scale all variables by one.
component_scale.resize (n_vars, 1.0);
}
// Resize the error_per_cell vectors to handle
// the number of elements, initialize them to 0.
std::vector<ErrorVectorReal> h_error_per_cell(mesh.max_elem_id(), 0.);
std::vector<ErrorVectorReal> p_error_per_cell(mesh.max_elem_id(), 0.);
// Loop over all the variables in the system
for (unsigned int var=0; var<n_vars; var++)
{
// Possibly skip this variable
if (!component_scale.empty())
if (component_scale[var] == 0.0) continue;
// The type of finite element to use for this variable
const FEType & fe_type = dof_map.variable_type (var);
// Finite element objects for a fine (and probably a coarse)
// element will be needed
fe = FEBase::build (dim, fe_type);
fe_coarse = FEBase::build (dim, fe_type);
// Any cached coarse element results have expired
coarse = libmesh_nullptr;
unsigned int cached_coarse_p_level = 0;
const FEContinuity cont = fe->get_continuity();
libmesh_assert (cont == DISCONTINUOUS || cont == C_ZERO ||
cont == C_ONE);
// Build an appropriate quadrature rule
qrule = fe_type.default_quadrature_rule(dim);
// Tell the refined finite element about the quadrature
// rule. The coarse finite element need not know about it
fe->attach_quadrature_rule (qrule.get());
// We will always do the integration
// on the fine elements. Get their Jacobian values, etc..
JxW = &(fe->get_JxW());
xyz_values = &(fe->get_xyz());
// The shape functions
phi = &(fe->get_phi());
phi_coarse = &(fe_coarse->get_phi());
// The shape function derivatives
if (cont == C_ZERO || cont == C_ONE)
{
dphi = &(fe->get_dphi());
dphi_coarse = &(fe_coarse->get_dphi());
}
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
// The shape function second derivatives
if (cont == C_ONE)
{
d2phi = &(fe->get_d2phi());
d2phi_coarse = &(fe_coarse->get_d2phi());
}
#endif // defined (LIBMESH_ENABLE_SECOND_DERIVATIVES)
// Iterate over all the active elements in the mesh
// that live on this processor.
MeshBase::const_element_iterator elem_it =
mesh.active_local_elements_begin();
const MeshBase::const_element_iterator elem_end =
mesh.active_local_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
// We're only checking elements that are already flagged for h
// refinement
if (elem->refinement_flag() != Elem::REFINE)
continue;
const dof_id_type e_id = elem->id();
// Find the projection onto the parent element,
// if necessary
if (elem->parent() &&
(coarse != elem->parent() ||
cached_coarse_p_level != elem->p_level()))
{
Uc.resize(0);
coarse = elem->parent();
cached_coarse_p_level = elem->p_level();
unsigned int old_parent_level = coarse->p_level();
(const_cast<Elem *>(coarse))->hack_p_level(elem->p_level());
this->add_projection(system, coarse, var);
(const_cast<Elem *>(coarse))->hack_p_level(old_parent_level);
// Solve the h-coarsening projection problem
Ke.cholesky_solve(Fe, Uc);
}
fe->reinit(elem);
// Get the DOF indices for the fine element
dof_map.dof_indices (elem, dof_indices, var);
// The number of quadrature points
const unsigned int n_qp = qrule->n_points();
// The number of DOFS on the fine element
const unsigned int n_dofs =
cast_int<unsigned int>(dof_indices.size());
// The number of nodes on the fine element
const unsigned int n_nodes = elem->n_nodes();
// The average element value (used as an ugly hack
// when we have nothing p-coarsened to compare to)
// Real average_val = 0.;
Number average_val = 0.;
// Calculate this variable's contribution to the p
// refinement error
if (elem->p_level() == 0)
{
unsigned int n_vertices = 0;
for (unsigned int n = 0; n != n_nodes; ++n)
if (elem->is_vertex(n))
{
n_vertices++;
const Node * const node = elem->get_node(n);
average_val += system.current_solution
(node->dof_number(sys_num,var,0));
}
average_val /= n_vertices;
}
else
{
unsigned int old_elem_level = elem->p_level();
(const_cast<Elem *>(elem))->hack_p_level(old_elem_level - 1);
fe_coarse->reinit(elem, &(qrule->get_points()));
const unsigned int n_coarse_dofs =
cast_int<unsigned int>(phi_coarse->size());
(const_cast<Elem *>(elem))->hack_p_level(old_elem_level);
Ke.resize(n_coarse_dofs, n_coarse_dofs);
Ke.zero();
Fe.resize(n_coarse_dofs);
Fe.zero();
// Loop over the quadrature points
for (unsigned int qp=0; qp<qrule->n_points(); qp++)
{
// The solution value at the quadrature point
Number val = libMesh::zero;
Gradient grad;
Tensor hess;
for (unsigned int i=0; i != n_dofs; i++)
{
dof_id_type dof_num = dof_indices[i];
val += (*phi)[i][qp] *
system.current_solution(dof_num);
if (cont == C_ZERO || cont == C_ONE)
grad.add_scaled((*dphi)[i][qp], system.current_solution(dof_num));
// grad += (*dphi)[i][qp] *
// system.current_solution(dof_num);
if (cont == C_ONE)
hess.add_scaled((*d2phi)[i][qp], system.current_solution(dof_num));
// hess += (*d2phi)[i][qp] *
// system.current_solution(dof_num);
}
// The projection matrix and vector
for (unsigned int i=0; i != Fe.size(); ++i)
{
Fe(i) += (*JxW)[qp] *
(*phi_coarse)[i][qp]*val;
if (cont == C_ZERO || cont == C_ONE)
Fe(i) += (*JxW)[qp] *
grad * (*dphi_coarse)[i][qp];
if (cont == C_ONE)
Fe(i) += (*JxW)[qp] *
hess.contract((*d2phi_coarse)[i][qp]);
for (unsigned int j=0; j != Fe.size(); ++j)
{
Ke(i,j) += (*JxW)[qp] *
(*phi_coarse)[i][qp]*(*phi_coarse)[j][qp];
if (cont == C_ZERO || cont == C_ONE)
Ke(i,j) += (*JxW)[qp] *
(*dphi_coarse)[i][qp]*(*dphi_coarse)[j][qp];
if (cont == C_ONE)
Ke(i,j) += (*JxW)[qp] *
((*d2phi_coarse)[i][qp].contract((*d2phi_coarse)[j][qp]));
}
}
}
// Solve the p-coarsening projection problem
Ke.cholesky_solve(Fe, Up);
}
// loop over the integration points on the fine element
for (unsigned int qp=0; qp<n_qp; qp++)
{
Number value_error = 0.;
Gradient grad_error;
Tensor hessian_error;
for (unsigned int i=0; i<n_dofs; i++)
{
const dof_id_type dof_num = dof_indices[i];
value_error += (*phi)[i][qp] *
system.current_solution(dof_num);
if (cont == C_ZERO || cont == C_ONE)
grad_error.add_scaled((*dphi)[i][qp], system.current_solution(dof_num));
// grad_error += (*dphi)[i][qp] *
// system.current_solution(dof_num);
if (cont == C_ONE)
hessian_error.add_scaled((*d2phi)[i][qp], system.current_solution(dof_num));
// hessian_error += (*d2phi)[i][qp] *
// system.current_solution(dof_num);
}
if (elem->p_level() == 0)
{
value_error -= average_val;
}
else
{
for (unsigned int i=0; i<Up.size(); i++)
{
value_error -= (*phi_coarse)[i][qp] * Up(i);
if (cont == C_ZERO || cont == C_ONE)
grad_error.subtract_scaled((*dphi_coarse)[i][qp], Up(i));
// grad_error -= (*dphi_coarse)[i][qp] * Up(i);
if (cont == C_ONE)
hessian_error.subtract_scaled((*d2phi_coarse)[i][qp], Up(i));
// hessian_error -= (*d2phi_coarse)[i][qp] * Up(i);
}
}
p_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * TensorTools::norm_sq(value_error));
if (cont == C_ZERO || cont == C_ONE)
p_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * grad_error.norm_sq());
if (cont == C_ONE)
p_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * hessian_error.norm_sq());
}
// Calculate this variable's contribution to the h
// refinement error
if (!elem->parent())
{
// For now, we'll always start with an h refinement
h_error_per_cell[e_id] =
std::numeric_limits<ErrorVectorReal>::max() / 2;
}
else
{
FEInterface::inverse_map (dim, fe_type, coarse,
*xyz_values, coarse_qpoints);
unsigned int old_parent_level = coarse->p_level();
(const_cast<Elem *>(coarse))->hack_p_level(elem->p_level());
fe_coarse->reinit(coarse, &coarse_qpoints);
(const_cast<Elem *>(coarse))->hack_p_level(old_parent_level);
// The number of DOFS on the coarse element
unsigned int n_coarse_dofs =
cast_int<unsigned int>(phi_coarse->size());
// Loop over the quadrature points
for (unsigned int qp=0; qp<n_qp; qp++)
{
// The solution difference at the quadrature point
Number value_error = libMesh::zero;
Gradient grad_error;
Tensor hessian_error;
for (unsigned int i=0; i != n_dofs; ++i)
{
const dof_id_type dof_num = dof_indices[i];
value_error += (*phi)[i][qp] *
system.current_solution(dof_num);
if (cont == C_ZERO || cont == C_ONE)
grad_error.add_scaled((*dphi)[i][qp], system.current_solution(dof_num));
// grad_error += (*dphi)[i][qp] *
// system.current_solution(dof_num);
if (cont == C_ONE)
hessian_error.add_scaled((*d2phi)[i][qp], system.current_solution(dof_num));
// hessian_error += (*d2phi)[i][qp] *
// system.current_solution(dof_num);
}
for (unsigned int i=0; i != n_coarse_dofs; ++i)
{
value_error -= (*phi_coarse)[i][qp] * Uc(i);
if (cont == C_ZERO || cont == C_ONE)
// grad_error -= (*dphi_coarse)[i][qp] * Uc(i);
grad_error.subtract_scaled((*dphi_coarse)[i][qp], Uc(i));
if (cont == C_ONE)
hessian_error.subtract_scaled((*d2phi_coarse)[i][qp], Uc(i));
// hessian_error -= (*d2phi_coarse)[i][qp] * Uc(i);
}
h_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * TensorTools::norm_sq(value_error));
if (cont == C_ZERO || cont == C_ONE)
h_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * grad_error.norm_sq());
if (cont == C_ONE)
h_error_per_cell[e_id] += static_cast<ErrorVectorReal>
(component_scale[var] *
(*JxW)[qp] * hessian_error.norm_sq());
}
}
}
}
// Now that we've got our approximations for p_error and h_error, let's see
// if we want to switch any h refinement flags to p refinement
// Iterate over all the active elements in the mesh
// that live on this processor.
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)
{
Elem * elem = *elem_it;
// We're only checking elements that are already flagged for h
// refinement
if (elem->refinement_flag() != Elem::REFINE)
continue;
const dof_id_type e_id = elem->id();
unsigned int dofs_per_elem = 0, dofs_per_p_elem = 0;
// Loop over all the variables in the system
for (unsigned int var=0; var<n_vars; var++)
{
// The type of finite element to use for this variable
const FEType & fe_type = dof_map.variable_type (var);
// FIXME: we're overestimating the number of DOFs added by h
// refinement
FEType elem_fe_type = fe_type;
elem_fe_type.order =
static_cast<Order>(fe_type.order + elem->p_level());
dofs_per_elem +=
FEInterface::n_dofs(dim, elem_fe_type, elem->type());
elem_fe_type.order =
static_cast<Order>(fe_type.order + elem->p_level() + 1);
dofs_per_p_elem +=
FEInterface::n_dofs(dim, elem_fe_type, elem->type());
}
const unsigned int new_h_dofs = dofs_per_elem *
(elem->n_children() - 1);
const unsigned int new_p_dofs = dofs_per_p_elem -
dofs_per_elem;
/*
libMesh::err << "Cell " << e_id << ": h = " << elem->hmax()
<< ", p = " << elem->p_level() + 1 << "," << std::endl
<< " h_error = " << h_error_per_cell[e_id]
<< ", p_error = " << p_error_per_cell[e_id] << std::endl
<< " new_h_dofs = " << new_h_dofs
<< ", new_p_dofs = " << new_p_dofs << std::endl;
*/
const Real p_value =
std::sqrt(p_error_per_cell[e_id]) * p_weight / new_p_dofs;
const Real h_value =
std::sqrt(h_error_per_cell[e_id]) /
static_cast<Real>(new_h_dofs);
if (p_value > h_value)
{
elem->set_p_refinement_flag(Elem::REFINE);
elem->set_refinement_flag(Elem::DO_NOTHING);
}
}
STOP_LOG("select_refinement()", "HPCoarsenTest");
}
void MeshRefinement::flag_elements_by_mean_stddev (const ErrorVector& error_per_cell,
const Real refine_frac,
const Real coarsen_frac,
const unsigned int max_l)
{
// The function arguments are currently just there for
// backwards_compatibility
if (!_use_member_parameters)
{
// If the user used non-default parameters, lets warn
// that they're deprecated
if (refine_frac != 0.3 ||
coarsen_frac != 0.0 ||
max_l != libMesh::invalid_uint)
libmesh_deprecated();
_refine_fraction = refine_frac;
_coarsen_fraction = coarsen_frac;
_max_h_level = max_l;
}
// Get the mean value from the error vector
const Real mean = error_per_cell.mean();
// Get the standard deviation. This equals the
// square-root of the variance
const Real stddev = std::sqrt (error_per_cell.variance());
// Check for valid fractions
libmesh_assert_greater_equal (_refine_fraction, 0);
libmesh_assert_less_equal (_refine_fraction, 1);
libmesh_assert_greater_equal (_coarsen_fraction, 0);
libmesh_assert_less_equal (_coarsen_fraction, 1);
// The refine and coarsen cutoff
const Real refine_cutoff = mean + _refine_fraction * stddev;
const Real coarsen_cutoff = std::max(mean - _coarsen_fraction * stddev, 0.);
// Loop over the elements and flag them for coarsening or
// refinement based on the element error
MeshBase::element_iterator elem_it = _mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = _mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
const unsigned int id = elem->id();
libmesh_assert_less (id, error_per_cell.size());
const float elem_error = error_per_cell[id];
// Possibly flag the element for coarsening ...
if (elem_error <= coarsen_cutoff)
elem->set_refinement_flag(Elem::COARSEN);
// ... or refinement
if ((elem_error >= refine_cutoff) && (elem->level() < _max_h_level))
elem->set_refinement_flag(Elem::REFINE);
}
}
// 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;
}
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 Elem::refine (MeshRefinement& mesh_refinement)
{
libmesh_assert (this->refinement_flag() == Elem::REFINE);
libmesh_assert (this->active());
// Create my children if necessary
if (!_children)
{
_children = new Elem*[this->n_children()];
unsigned int parent_p_level = this->p_level();
for (unsigned int c=0; c<this->n_children(); c++)
{
_children[c] = Elem::build(this->type(), this).release();
_children[c]->set_refinement_flag(Elem::JUST_REFINED);
_children[c]->set_p_level(parent_p_level);
_children[c]->set_p_refinement_flag(this->p_refinement_flag());
}
// Compute new nodal locations
// and asssign nodes to children
// Make these static. It is unlikely the
// sizes will change from call to call, so having these
// static should save on reallocations
std::vector<std::vector<Point> > p (this->n_children());
std::vector<std::vector<Node*> > nodes(this->n_children());
// compute new nodal locations
for (unsigned int c=0; c<this->n_children(); c++)
{
Elem *child = this->child(c);
p[c].resize (child->n_nodes());
nodes[c].resize(child->n_nodes());
for (unsigned int nc=0; nc<child->n_nodes(); nc++)
{
// zero entries
p[c][nc].zero();
nodes[c][nc] = NULL;
for (unsigned int n=0; n<this->n_nodes(); n++)
{
// The value from the embedding matrix
const float em_val = this->embedding_matrix(c,nc,n);
if (em_val != 0.)
{
p[c][nc].add_scaled (this->point(n), em_val);
// We may have found the node, in which case we
// won't need to look it up later.
if (em_val == 1.)
nodes[c][nc] = this->get_node(n);
}
}
}
// assign nodes to children & add them to the mesh
const Real pointtol = this->hmin() * TOLERANCE;
for (unsigned int nc=0; nc<child->n_nodes(); nc++)
{
if (nodes[c][nc] != NULL)
{
child->set_node(nc) = nodes[c][nc];
}
else
{
child->set_node(nc) =
mesh_refinement.add_point(p[c][nc],
child->processor_id(),
pointtol);
child->get_node(nc)->set_n_systems
(this->n_systems());
}
}
mesh_refinement.add_elem (child);
child->set_n_systems(this->n_systems());
}
}
else
{
unsigned int parent_p_level = this->p_level();
for (unsigned int c=0; c<this->n_children(); c++)
{
Elem *child = this->child(c);
libmesh_assert(child->subactive());
child->set_refinement_flag(Elem::JUST_REFINED);
child->set_p_level(parent_p_level);
child->set_p_refinement_flag(this->p_refinement_flag());
}
}
// Un-set my refinement flag now
this->set_refinement_flag(Elem::INACTIVE);
this->set_p_refinement_flag(Elem::INACTIVE);
for (unsigned int c=0; c<this->n_children(); c++)
{
libmesh_assert(this->child(c)->parent() == this);
libmesh_assert(this->child(c)->active());
}
libmesh_assert (this->ancestor());
}
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;
}