void ElemCutter::cut_2D (const Elem & elem,
const std::vector<Real> & vertex_distance_func)
{
#ifndef LIBMESH_HAVE_TRIANGLE
// current implementation requires triangle!
libMesh::err << "ERROR: current libMesh ElemCutter 2D implementation requires\n"
<< " the \"triangle\" library!\n"
<< std::endl;
libmesh_not_implemented();
#else // OK, LIBMESH_HAVE_TRIANGLE
std::cout << "Inside cut face element!\n";
libmesh_assert (_inside_mesh_2D.get() != nullptr);
libmesh_assert (_outside_mesh_2D.get() != nullptr);
_inside_mesh_2D->clear();
_outside_mesh_2D->clear();
for (unsigned int v=0; v<elem.n_vertices(); v++)
{
if (vertex_distance_func[v] >= 0.)
_outside_mesh_2D->add_point (elem.point(v));
if (vertex_distance_func[v] <= 0.)
_inside_mesh_2D->add_point (elem.point(v));
}
for (const auto & pt : _intersection_pts)
{
_inside_mesh_2D->add_point(pt);
_outside_mesh_2D->add_point(pt);
}
// Customize the variables for the triangulation
// we will be cutting reference cell, and want as few triangles
// as possible, so jack this up larger than the area we will be
// triangulating so we are governed only by accurately defining
// the boundaries.
_triangle_inside->desired_area() = 100.;
_triangle_outside->desired_area() = 100.;
// allow for small angles
_triangle_inside->minimum_angle() = 5.;
_triangle_outside->minimum_angle() = 5.;
// Turn off Laplacian mesh smoothing after generation.
_triangle_inside->smooth_after_generating() = false;
_triangle_outside->smooth_after_generating() = false;
// Triangulate!
_triangle_inside->triangulate();
_triangle_outside->triangulate();
// std::ostringstream name;
// name << "cut_face_"
// << cut_cntr++
// << ".dat";
// _inside_mesh_2D->write ("in_" + name.str());
// _outside_mesh_2D->write ("out_" + name.str());
// finally, add the elements to our lists.
_inside_elem.clear();
_outside_elem.clear();
for (const auto & elem : _inside_mesh_2D->element_ptr_range())
_inside_elem.push_back (elem);
for (const auto & elem : _outside_mesh_2D->element_ptr_range())
_outside_elem.push_back (elem);
#endif
}
void ElemCutter::cut_3D (const Elem & elem,
const std::vector<Real> & vertex_distance_func)
{
#ifndef LIBMESH_HAVE_TETGEN
// current implementation requires tetgen!
libMesh::err << "ERROR: current libMesh ElemCutter 3D implementation requires\n"
<< " the \"tetgen\" library!\n"
<< std::endl;
libmesh_not_implemented();
#else // OK, LIBMESH_HAVE_TETGEN
std::cout << "Inside cut cell element!\n";
libmesh_assert (_inside_mesh_3D.get() != nullptr);
libmesh_assert (_outside_mesh_3D.get() != nullptr);
_inside_mesh_3D->clear();
_outside_mesh_3D->clear();
for (unsigned int v=0; v<elem.n_vertices(); v++)
{
if (vertex_distance_func[v] >= 0.)
_outside_mesh_3D->add_point (elem.point(v));
if (vertex_distance_func[v] <= 0.)
_inside_mesh_3D->add_point (elem.point(v));
}
for (const auto & pt : _intersection_pts)
{
_inside_mesh_3D->add_point(pt);
_outside_mesh_3D->add_point(pt);
}
// Triangulate!
_tetgen_inside->triangulate_pointset();
//_inside_mesh_3D->print_info();
_tetgen_outside->triangulate_pointset();
//_outside_mesh_3D->print_info();
// (below generates some horribly expensive meshes,
// but seems immune to the 0 volume problem).
// _tetgen_inside->pointset_convexhull();
// _inside_mesh_3D->find_neighbors();
// _inside_mesh_3D->print_info();
// _tetgen_inside->triangulate_conformingDelaunayMesh (1.e3, 100.);
// _inside_mesh_3D->print_info();
// _tetgen_outside->pointset_convexhull();
// _outside_mesh_3D->find_neighbors();
// _outside_mesh_3D->print_info();
// _tetgen_outside->triangulate_conformingDelaunayMesh (1.e3, 100.);
// _outside_mesh_3D->print_info();
std::ostringstream name;
name << "cut_cell_"
<< cut_cntr++
<< ".dat";
_inside_mesh_3D->write ("in_" + name.str());
_outside_mesh_3D->write ("out_" + name.str());
// finally, add the elements to our lists.
_inside_elem.clear();
_outside_elem.clear();
for (const auto & elem : _inside_mesh_3D->element_ptr_range())
if (elem->volume() > std::numeric_limits<Real>::epsilon())
_inside_elem.push_back (elem);
for (const auto & elem : _outside_mesh_3D->element_ptr_range())
if (elem->volume() > std::numeric_limits<Real>::epsilon())
_outside_elem.push_back (elem);
#endif
}
// 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 MeshTools::Subdivision::add_boundary_ghosts(MeshBase & mesh)
{
static const Real tol = 1e-5;
// add the mirrored ghost elements (without using iterators, because the mesh is modified in the course)
std::vector<Tri3Subdivision *> ghost_elems;
std::vector<Node *> ghost_nodes;
const unsigned int n_elem = mesh.n_elem();
for (unsigned int eid = 0; eid < n_elem; ++eid)
{
Elem * elem = mesh.elem(eid);
libmesh_assert_equal_to(elem->type(), TRI3SUBDIVISION);
// If the triangle happens to be in a corner (two boundary
// edges), we perform a counter-clockwise loop by mirroring the
// previous triangle until we come back to the original
// triangle. This prevents degenerated triangles in the mesh
// corners and guarantees that the node in the middle of the
// loop is of valence=6.
for (unsigned int i = 0; i < elem->n_sides(); ++i)
{
libmesh_assert_not_equal_to(elem->neighbor(i), elem);
if (elem->neighbor(i) == libmesh_nullptr &&
elem->neighbor(next[i]) == libmesh_nullptr)
{
Elem * nelem = elem;
unsigned int k = i;
for (unsigned int l=0;l<4;l++)
{
// this is the vertex to be mirrored
Point point = nelem->point(k) + nelem->point(next[k]) - nelem->point(prev[k]);
// Check if the proposed vertex doesn't coincide
// with one of the existing vertices. This is
// necessary because for some triangulations, it can
// happen that two mirrored ghost vertices coincide,
// which would then lead to a zero size ghost
// element below.
Node * node = libmesh_nullptr;
for (unsigned int j = 0; j < ghost_nodes.size(); ++j)
{
if ((*ghost_nodes[j] - point).size() < tol * (elem->point(k) - point).size())
{
node = ghost_nodes[j];
break;
}
}
// add the new vertex only if no other is nearby
if (node == libmesh_nullptr)
{
node = mesh.add_point(point);
ghost_nodes.push_back(node);
}
Tri3Subdivision * newelem = new Tri3Subdivision();
// add the first new ghost element to the list just as in the non-corner case
if (l == 0)
ghost_elems.push_back(newelem);
newelem->set_node(0) = nelem->get_node(next[k]);
newelem->set_node(1) = nelem->get_node(k);
newelem->set_node(2) = node;
newelem->set_neighbor(0, nelem);
newelem->set_ghost(true);
if (l>0)
newelem->set_neighbor(2, libmesh_nullptr);
nelem->set_neighbor(k, newelem);
mesh.add_elem(newelem);
mesh.get_boundary_info().add_node(nelem->get_node(k), 1);
mesh.get_boundary_info().add_node(nelem->get_node(next[k]), 1);
mesh.get_boundary_info().add_node(nelem->get_node(prev[k]), 1);
mesh.get_boundary_info().add_node(node, 1);
nelem = newelem;
k = 2 ;
}
Tri3Subdivision * newelem = new Tri3Subdivision();
newelem->set_node(0) = elem->get_node(next[i]);
newelem->set_node(1) = nelem->get_node(2);
newelem->set_node(2) = elem->get_node(prev[i]);
newelem->set_neighbor(0, nelem);
nelem->set_neighbor(2, newelem);
newelem->set_ghost(true);
newelem->set_neighbor(2, elem);
elem->set_neighbor(next[i],newelem);
mesh.add_elem(newelem);
break;
}
}
for (unsigned int i = 0; i < elem->n_sides(); ++i)
{
libmesh_assert_not_equal_to(elem->neighbor(i), elem);
if (elem->neighbor(i) == libmesh_nullptr)
{
// this is the vertex to be mirrored
Point point = elem->point(i) + elem->point(next[i]) - elem->point(prev[i]);
// Check if the proposed vertex doesn't coincide with
// one of the existing vertices. This is necessary
// because for some triangulations, it can happen that
// two mirrored ghost vertices coincide, which would
// then lead to a zero size ghost element below.
Node * node = libmesh_nullptr;
for (unsigned int j = 0; j < ghost_nodes.size(); ++j)
{
if ((*ghost_nodes[j] - point).size() < tol * (elem->point(i) - point).size())
{
node = ghost_nodes[j];
break;
}
}
// add the new vertex only if no other is nearby
if (node == libmesh_nullptr)
{
node = mesh.add_point(point);
ghost_nodes.push_back(node);
}
Tri3Subdivision * newelem = new Tri3Subdivision();
ghost_elems.push_back(newelem);
newelem->set_node(0) = elem->get_node(next[i]);
newelem->set_node(1) = elem->get_node(i);
newelem->set_node(2) = node;
newelem->set_neighbor(0, elem);
newelem->set_ghost(true);
elem->set_neighbor(i, newelem);
mesh.add_elem(newelem);
mesh.get_boundary_info().add_node(elem->get_node(i), 1);
mesh.get_boundary_info().add_node(elem->get_node(next[i]), 1);
mesh.get_boundary_info().add_node(elem->get_node(prev[i]), 1);
mesh.get_boundary_info().add_node(node, 1);
}
}
}
// add the missing ghost elements (connecting new ghost nodes)
std::vector<Tri3Subdivision *> missing_ghost_elems;
std::vector<Tri3Subdivision *>::iterator ghost_el = ghost_elems.begin();
const std::vector<Tri3Subdivision *>::iterator end_ghost_el = ghost_elems.end();
for (; ghost_el != end_ghost_el; ++ghost_el)
{
Tri3Subdivision * elem = *ghost_el;
libmesh_assert(elem->is_ghost());
for (unsigned int i = 0; i < elem->n_sides(); ++i)
{
if (elem->neighbor(i) == libmesh_nullptr &&
elem->neighbor(prev[i]) != libmesh_nullptr)
{
// go around counter-clockwise
Tri3Subdivision * nb1 = static_cast<Tri3Subdivision *>(elem->neighbor(prev[i]));
Tri3Subdivision * nb2 = nb1;
unsigned int j = i;
unsigned int n_nb = 0;
while (nb1 != libmesh_nullptr && nb1->id() != elem->id())
{
j = nb1->local_node_number(elem->node(i));
nb2 = nb1;
nb1 = static_cast<Tri3Subdivision *>(nb1->neighbor(prev[j]));
libmesh_assert(nb1 == libmesh_nullptr || nb1->id() != nb2->id());
n_nb++;
}
libmesh_assert_not_equal_to(nb2->id(), elem->id());
// Above, we merged coinciding ghost vertices. Therefore, we need
// to exclude the case where there is no ghost element to add between
// these two (identical) ghost nodes.
if (elem->get_node(next[i])->id() == nb2->get_node(prev[j])->id())
break;
// If the number of already present neighbors is less than 4, we add another extra element
// so that the node in the middle of the loop ends up being of valence=6.
// This case usually happens when the middle node corresponds to a corner of the original mesh,
// and the extra element below prevents degenerated triangles in the mesh corners.
if (n_nb < 4)
{
// this is the vertex to be mirrored
Point point = nb2->point(j) + nb2->point(prev[j]) - nb2->point(next[j]);
// Check if the proposed vertex doesn't coincide with one of the existing vertices.
// This is necessary because for some triangulations, it can happen that two mirrored
// ghost vertices coincide, which would then lead to a zero size ghost element below.
Node * node = libmesh_nullptr;
for (unsigned int k = 0; k < ghost_nodes.size(); ++k)
{
if ((*ghost_nodes[k] - point).size() < tol * (nb2->point(j) - point).size())
{
node = ghost_nodes[k];
break;
}
}
// add the new vertex only if no other is nearby
if (node == libmesh_nullptr)
{
node = mesh.add_point(point);
ghost_nodes.push_back(node);
}
Tri3Subdivision * newelem = new Tri3Subdivision();
newelem->set_node(0) = nb2->get_node(j);
newelem->set_node(1) = nb2->get_node(prev[j]);
newelem->set_node(2) = node;
newelem->set_neighbor(0, nb2);
newelem->set_neighbor(1, libmesh_nullptr);
newelem->set_ghost(true);
nb2->set_neighbor(prev[j], newelem);
mesh.add_elem(newelem);
mesh.get_boundary_info().add_node(nb2->get_node(j), 1);
mesh.get_boundary_info().add_node(nb2->get_node(prev[j]), 1);
mesh.get_boundary_info().add_node(node, 1);
nb2 = newelem;
j = nb2->local_node_number(elem->node(i));
}
Tri3Subdivision * newelem = new Tri3Subdivision();
newelem->set_node(0) = elem->get_node(next[i]);
newelem->set_node(1) = elem->get_node(i);
newelem->set_node(2) = nb2->get_node(prev[j]);
newelem->set_neighbor(0, elem);
newelem->set_neighbor(1, nb2);
newelem->set_neighbor(2, libmesh_nullptr);
newelem->set_ghost(true);
elem->set_neighbor(i, newelem);
nb2->set_neighbor(prev[j], newelem);
missing_ghost_elems.push_back(newelem);
break;
}
} // end side loop
} // end ghost element loop
// add the missing ghost elements to the mesh
std::vector<Tri3Subdivision *>::iterator missing_el = missing_ghost_elems.begin();
const std::vector<Tri3Subdivision *>::iterator end_missing_el = missing_ghost_elems.end();
for (; missing_el != end_missing_el; ++missing_el)
mesh.add_elem(*missing_el);
}
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
}
int main(int argc, char** argv){
// Initilize libMesh
LibMeshInit init (argc, argv);
// Create the mesh, single element
Mesh mesh;
MeshTools::Generation::build_square(mesh, 1, 1, -1, 1, -1, 1, QUAD4);
// Create an equation system
EquationSystems eq_sys(mesh);
// Create the equation systems via shared_ptr pointers
boost::shared_ptr<ThermoEq> thermo(new ThermoEq(eq_sys));
boost::shared_ptr<MomentumEq> momentum(new MomentumEq(eq_sys, FIRST));
boost::shared_ptr<ConcentrationEq> concentration(new ConcentrationEq(eq_sys, FIRST));
boost::shared_ptr<EnergyEq> energy(new EnergyEq(eq_sys, FIRST));
// Link the initialization functions
momentum->add_initial_function(initial_velocity);
concentration->add_initial_function(initial_concentration);
energy->add_initial_function(initial_temperature);
// Add the necessary cross-linking between the systems via their pointers
thermo->momentum = momentum;
thermo->energy = energy;
thermo->concentration = concentration;
energy->thermo = thermo;
energy->momentum = momentum;
// Initialize the various systems
momentum->init();
concentration->init();
energy->init();
thermo->init();
// Get a pointer to the first (and only) element
Elem* elem = mesh.elem(0);
// Display the values for initial enthalpy; computed from temp.
printf("\n\nTEMP. TO ENTHALPY CONVERSION:\n");
for (unsigned int i = 0; i < elem->n_nodes(); i++){
Point& p = elem->point(i);
Number h = energy->point_value(0,p);
printf("\th = %g (%g, %g)\n", h, p(0), p(1));
}
// thermo->test(elem);
// DenseVector<Number> output(1);
//energy.enthalpy(output, p, 0.0);
//energy.init();
// Thermodynamics links
//data.init();
//printf("initilized = %s\n", (data.velocity_ptr->initialized())?"true":"false");
/*
// Print some basic element information
printf("\n\nELEMENT INFORMATION:\n");
// Test that values are correct, use first (only) element
VectorValue<Number> v;
Elem* elem = mesh.elem(0);
for (unsigned int i = 0; i < elem->n_nodes(); i++){
Point& p = elem->point(i);
v = data.velocity_ptr->point_value(p);
printf("\tPoint %g, %g\tv = %g, %g\n", p(0),p(1),v(0),v(1));
}
// Test the element length
printf("\nTESTING: element data\n");
Number h = data.element_length(elem);
printf("\tElement length (%f): %f\n", 1.065004, h);
// Test the tau_1 value
printf("\nTESTING: Tau_1\n");
printf("\tTau_1: %g\n", data.tau_1(elem->point(0), data.element_length(elem)));
printf("\tTau_1: %g\n", data.tau_1(elem->point(1), data.element_length(elem)));
printf("\tTau_1: %g\n", data.tau_1(elem->point(2), data.element_length(elem)));
printf("\tTau_1: %g\n", data.tau_1(elem->point(3), data.element_length(elem)));
*/
// Test the EnergyEq assembly
printf("\nTESTING: energy eq. assembly\n");
energy->assemble();
}
void Elem::coarsen()
{
libmesh_assert_equal_to (this->refinement_flag(), Elem::COARSEN_INACTIVE);
libmesh_assert (!this->active());
// We no longer delete children until MeshRefinement::contract()
// delete [] _children;
// _children = nullptr;
unsigned int parent_p_level = 0;
// re-compute hanging node nodal locations
for (unsigned int c = 0, nc = this->n_children(); c != nc; ++c)
{
Elem * mychild = this->child_ptr(c);
if (mychild == remote_elem)
continue;
for (unsigned int cnode=0; cnode != mychild->n_nodes(); ++cnode)
{
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,cnode,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->point(cnode);
child_node(i)=new_pos(i);
}
}
}
}
for (auto & mychild : this->child_ref_range())
{
if (&mychild == remote_elem)
continue;
libmesh_assert_equal_to (mychild.refinement_flag(), Elem::COARSEN);
mychild.set_refinement_flag(Elem::INACTIVE);
if (mychild.p_level() > parent_p_level)
parent_p_level = mychild.p_level();
}
this->set_refinement_flag(Elem::JUST_COARSENED);
this->set_p_level(parent_p_level);
libmesh_assert (this->active());
}