//-----------------------------------------------------------------
// 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);
}
}
void InfPrism12::connectivity(const unsigned int sc,
const IOPackage iop,
std::vector<dof_id_type>& conn) const
{
libmesh_assert(_nodes);
libmesh_assert_less (sc, this->n_sub_elem());
libmesh_assert_not_equal_to (iop, INVALID_IO_PACKAGE);
switch (iop)
{
case TECPLOT:
{
conn.resize(8);
switch (sc)
{
case 0:
// guess this is a collapsed hex8
conn[0] = this->node(0)+1;
conn[1] = this->node(6)+1;
conn[2] = this->node(8)+1;
conn[3] = this->node(8)+1;
conn[4] = this->node(3)+1;
conn[5] = this->node(9)+1;
conn[6] = this->node(11)+1;
conn[7] = this->node(11)+1;
return;
case 1:
conn[0] = this->node(6)+1;
conn[1] = this->node(7)+1;
conn[2] = this->node(8)+1;
conn[3] = this->node(8)+1;
conn[4] = this->node(9)+1;
conn[5] = this->node(10)+1;
conn[6] = this->node(11)+1;
conn[7] = this->node(11)+1;
return;
case 2:
conn[0] = this->node(6)+1;
conn[1] = this->node(1)+1;
conn[2] = this->node(7)+1;
conn[3] = this->node(7)+1;
conn[4] = this->node(9)+1;
conn[5] = this->node(4)+1;
conn[6] = this->node(10)+1;
conn[7] = this->node(10)+1;
return;
case 3:
conn[0] = this->node(8)+1;
conn[1] = this->node(7)+1;
conn[2] = this->node(2)+1;
conn[3] = this->node(2)+1;
conn[4] = this->node(11)+1;
conn[5] = this->node(10)+1;
conn[6] = this->node(5)+1;
conn[7] = this->node(5)+1;
return;
default:
libmesh_error();
}
}
default:
libmesh_error();
}
libmesh_error();
}
RealGradient FE<2,NEDELEC_ONE>::shape_second_deriv(const Elem* elem,
const Order order,
const unsigned int i,
const unsigned int j,
const Point&)
{
#if LIBMESH_DIM > 1
libmesh_assert(elem);
// j = 0 ==> d^2 phi / dxi^2
// j = 1 ==> d^2 phi / dxi deta
// j = 2 ==> d^2 phi / deta^2
libmesh_assert_less (j, 3);
const Order total_order = static_cast<Order>(order + elem->p_level());
switch (total_order)
{
// linear Lagrange shape functions
case FIRST:
{
switch (elem->type())
{
case QUAD8:
case QUAD9:
{
libmesh_assert_less (i, 4);
// All second derivatives for linear quads are zero.
return RealGradient();
}
case TRI6:
{
libmesh_assert_less (i, 3);
// All second derivatives for linear triangles are zero.
return RealGradient();
}
default:
{
libMesh::err << "ERROR: Unsupported 2D element type!: " << elem->type()
<< std::endl;
libmesh_error();
}
} // end switch (type)
} // end case FIRST
// unsupported order
default:
{
libMesh::err << "ERROR: Unsupported 2D FE order!: " << total_order
<< std::endl;
libmesh_error();
}
} // end switch (order)
#endif // LIBMESH_DIM > 1
libmesh_error();
return RealGradient();
}
void InfHex18::connectivity(const unsigned int sc,
const IOPackage iop,
std::vector<dof_id_type>& conn) const
{
libmesh_assert(_nodes);
libmesh_assert_less (sc, this->n_sub_elem());
libmesh_assert_not_equal_to (iop, INVALID_IO_PACKAGE);
switch (iop)
{
case TECPLOT:
{
switch (sc)
{
case 0:
conn[0] = this->node(0)+1;
conn[1] = this->node(8)+1;
conn[2] = this->node(16)+1;
conn[3] = this->node(11)+1;
conn[4] = this->node(4)+1;
conn[5] = this->node(12)+1;
conn[6] = this->node(17)+1;
conn[7] = this->node(15)+1;
return;
case 1:
conn[0] = this->node(8)+1;
conn[1] = this->node(1)+1;
conn[2] = this->node(9)+1;
conn[3] = this->node(16)+1;
conn[4] = this->node(12)+1;
conn[5] = this->node(5)+1;
conn[6] = this->node(13)+1;
conn[7] = this->node(17)+1;
return;
case 2:
conn[0] = this->node(11)+1;
conn[1] = this->node(16)+1;
conn[2] = this->node(10)+1;
conn[3] = this->node(3)+1;
conn[4] = this->node(15)+1;
conn[5] = this->node(17)+1;
conn[6] = this->node(14)+1;
conn[7] = this->node(7)+1;
return;
case 3:
conn[0] = this->node(16)+1;
conn[1] = this->node(9)+1;
conn[2] = this->node(2)+1;
conn[3] = this->node(10)+1;
conn[4] = this->node(17)+1;
conn[5] = this->node(13)+1;
conn[6] = this->node(6)+1;
conn[7] = this->node(14)+1;
return;
default:
libmesh_error_msg("Invalid sc = " << sc);
}
}
default:
libmesh_error_msg("Unsupported IO package " << iop);
}
}
bool InfEdge2::is_node_on_side(const unsigned int n,
const unsigned int s) const
{
libmesh_assert_less (s, 1);
return (s == n);
}
AutoPtr<Elem> Tet10::build_side (const unsigned int i,
bool proxy) const
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
AutoPtr<Elem> ap(new Side<Tri6,Tet10>(this,i));
return ap;
}
else
{
AutoPtr<Elem> face(new Tri6);
switch (i)
{
case 0:
{
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(2);
face->set_node(2) = this->get_node(1);
face->set_node(3) = this->get_node(6);
face->set_node(4) = this->get_node(5);
face->set_node(5) = this->get_node(4);
return face;
}
case 1:
{
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(3);
face->set_node(3) = this->get_node(4);
face->set_node(4) = this->get_node(8);
face->set_node(5) = this->get_node(7);
return face;
}
case 2:
{
face->set_node(0) = this->get_node(1);
face->set_node(1) = this->get_node(2);
face->set_node(2) = this->get_node(3);
face->set_node(3) = this->get_node(5);
face->set_node(4) = this->get_node(9);
face->set_node(5) = this->get_node(8);
return face;
}
case 3:
{
face->set_node(0) = this->get_node(2);
face->set_node(1) = this->get_node(0);
face->set_node(2) = this->get_node(3);
face->set_node(3) = this->get_node(6);
face->set_node(4) = this->get_node(7);
face->set_node(5) = this->get_node(9);
return face;
}
default:
{
libmesh_error();
}
}
}
// We'll never get here.
libmesh_error();
AutoPtr<Elem> ap(NULL); return ap;
}
void Tet10::connectivity(const unsigned int sc,
const IOPackage iop,
std::vector<unsigned int>& conn) const
{
libmesh_assert(_nodes);
libmesh_assert_less (sc, this->n_sub_elem());
libmesh_assert_not_equal_to (iop, INVALID_IO_PACKAGE);
switch (iop)
{
case TECPLOT:
{
conn.resize(8);
switch (sc)
{
// Linear sub-tet 0
case 0:
conn[0] = this->node(0)+1;
conn[1] = this->node(4)+1;
conn[2] = this->node(6)+1;
conn[3] = this->node(6)+1;
conn[4] = this->node(7)+1;
conn[5] = this->node(7)+1;
conn[6] = this->node(7)+1;
conn[7] = this->node(7)+1;
return;
// Linear sub-tet 1
case 1:
conn[0] = this->node(4)+1;
conn[1] = this->node(1)+1;
conn[2] = this->node(5)+1;
conn[3] = this->node(5)+1;
conn[4] = this->node(8)+1;
conn[5] = this->node(8)+1;
conn[6] = this->node(8)+1;
conn[7] = this->node(8)+1;
return;
// Linear sub-tet 2
case 2:
conn[0] = this->node(5)+1;
conn[1] = this->node(2)+1;
conn[2] = this->node(6)+1;
conn[3] = this->node(6)+1;
conn[4] = this->node(9)+1;
conn[5] = this->node(9)+1;
conn[6] = this->node(9)+1;
conn[7] = this->node(9)+1;
return;
// Linear sub-tet 3
case 3:
conn[0] = this->node(7)+1;
conn[1] = this->node(8)+1;
conn[2] = this->node(9)+1;
conn[3] = this->node(9)+1;
conn[4] = this->node(3)+1;
conn[5] = this->node(3)+1;
conn[6] = this->node(3)+1;
conn[7] = this->node(3)+1;
return;
// Linear sub-tet 4
case 4:
conn[0] = this->node(4)+1;
conn[1] = this->node(8)+1;
conn[2] = this->node(6)+1;
conn[3] = this->node(6)+1;
conn[4] = this->node(7)+1;
conn[5] = this->node(7)+1;
conn[6] = this->node(7)+1;
conn[7] = this->node(7)+1;
return;
// Linear sub-tet 5
case 5:
conn[0] = this->node(4)+1;
conn[1] = this->node(5)+1;
conn[2] = this->node(6)+1;
conn[3] = this->node(6)+1;
conn[4] = this->node(8)+1;
conn[5] = this->node(8)+1;
conn[6] = this->node(8)+1;
conn[7] = this->node(8)+1;
return;
// Linear sub-tet 6
case 6:
conn[0] = this->node(5)+1;
conn[1] = this->node(9)+1;
conn[2] = this->node(6)+1;
conn[3] = this->node(6)+1;
conn[4] = this->node(8)+1;
conn[5] = this->node(8)+1;
conn[6] = this->node(8)+1;
conn[7] = this->node(8)+1;
return;
// Linear sub-tet 7
case 7:
conn[0] = this->node(7)+1;
conn[1] = this->node(6)+1;
conn[2] = this->node(9)+1;
conn[3] = this->node(9)+1;
conn[4] = this->node(8)+1;
conn[5] = this->node(8)+1;
conn[6] = this->node(8)+1;
conn[7] = this->node(8)+1;
return;
default:
libmesh_error();
}
}
case VTK:
{
conn.resize(10);
conn[0] = this->node(0);
conn[1] = this->node(1);
conn[2] = this->node(2);
conn[3] = this->node(3);
conn[4] = this->node(4);
conn[5] = this->node(5);
conn[6] = this->node(6);
conn[7] = this->node(7);
conn[8] = this->node(8);
conn[9] = this->node(9);
return;
/*
conn.resize(4);
switch (sc)
{
// Linear sub-tet 0
case 0:
conn[0] = this->node(0);
conn[1] = this->node(4);
conn[2] = this->node(6);
conn[3] = this->node(7);
return;
// Linear sub-tet 1
case 1:
conn[0] = this->node(4);
conn[1] = this->node(1);
conn[2] = this->node(5);
conn[3] = this->node(8);
return;
// Linear sub-tet 2
case 2:
conn[0] = this->node(5);
conn[1] = this->node(2);
conn[2] = this->node(6);
conn[3] = this->node(9);
return;
// Linear sub-tet 3
case 3:
conn[0] = this->node(7);
conn[1] = this->node(8);
conn[2] = this->node(9);
conn[3] = this->node(3);
return;
// Linear sub-tet 4
case 4:
conn[0] = this->node(4);
conn[1] = this->node(8);
conn[2] = this->node(6);
conn[3] = this->node(7);
return;
// Linear sub-tet 5
case 5:
conn[0] = this->node(4);
conn[1] = this->node(5);
conn[2] = this->node(6);
conn[3] = this->node(8);
return;
// Linear sub-tet 6
case 6:
conn[0] = this->node(5);
conn[1] = this->node(9);
conn[2] = this->node(6);
conn[3] = this->node(8);
return;
// Linear sub-tet 7
case 7:
conn[0] = this->node(7);
conn[1] = this->node(6);
conn[2] = this->node(9);
conn[3] = this->node(8);
return;
default:
libmesh_error();
}
*/
}
default:
libmesh_error();
}
libmesh_error();
}
AutoPtr<Elem> Prism15::build_side (const unsigned int i,
bool proxy) const
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
switch (i)
{
case 0: // the triangular face at z=-1
case 4:
{
AutoPtr<Elem> face(new Side<Tri6,Prism15>(this,i));
return face;
}
case 1:
case 2:
case 3:
{
AutoPtr<Elem> face(new Side<Quad8,Prism15>(this,i));
return face;
}
default:
{
libmesh_error();
}
}
}
else
{
// Create NULL pointer to be initialized, returned later.
AutoPtr<Elem> face(NULL);
switch (i)
{
case 0: // the triangular face at z=-1
{
face.reset(new Tri6);
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(2);
face->set_node(2) = this->get_node(1);
face->set_node(3) = this->get_node(8);
face->set_node(4) = this->get_node(7);
face->set_node(5) = this->get_node(6);
break;
}
case 1: // the quad face at y=0
{
face.reset(new Quad8);
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(4);
face->set_node(3) = this->get_node(3);
face->set_node(4) = this->get_node(6);
face->set_node(5) = this->get_node(10);
face->set_node(6) = this->get_node(12);
face->set_node(7) = this->get_node(9);
break;
}
case 2: // the other quad face
{
face.reset(new Quad8);
face->set_node(0) = this->get_node(1);
face->set_node(1) = this->get_node(2);
face->set_node(2) = this->get_node(5);
face->set_node(3) = this->get_node(4);
face->set_node(4) = this->get_node(7);
face->set_node(5) = this->get_node(11);
face->set_node(6) = this->get_node(13);
face->set_node(7) = this->get_node(10);
break;
}
case 3: // the quad face at x=0
{
face.reset(new Quad8);
face->set_node(0) = this->get_node(2);
face->set_node(1) = this->get_node(0);
face->set_node(2) = this->get_node(3);
face->set_node(3) = this->get_node(5);
face->set_node(4) = this->get_node(8);
face->set_node(5) = this->get_node(9);
face->set_node(6) = this->get_node(14);
face->set_node(7) = this->get_node(11);
break;
}
case 4: // the triangular face at z=1
{
face.reset(new Tri6);
face->set_node(0) = this->get_node(3);
face->set_node(1) = this->get_node(4);
face->set_node(2) = this->get_node(5);
face->set_node(3) = this->get_node(12);
face->set_node(4) = this->get_node(13);
face->set_node(5) = this->get_node(14);
break;
}
default:
{
libmesh_error();
}
}
face->subdomain_id() = this->subdomain_id();
return face;
}
// We'll never get here.
libmesh_error();
AutoPtr<Elem> ap(NULL); return ap;
}
void Prism15::connectivity(const unsigned int libmesh_dbg_var(sc),
const IOPackage iop,
std::vector<dof_id_type>& conn) const
{
libmesh_assert(_nodes);
libmesh_assert_less (sc, this->n_sub_elem());
libmesh_assert_not_equal_to (iop, INVALID_IO_PACKAGE);
switch (iop)
{
case TECPLOT:
{
conn.resize(8);
conn[0] = this->node(0)+1;
conn[1] = this->node(1)+1;
conn[2] = this->node(2)+1;
conn[3] = this->node(2)+1;
conn[4] = this->node(3)+1;
conn[5] = this->node(4)+1;
conn[6] = this->node(5)+1;
conn[7] = this->node(5)+1;
return;
}
case VTK:
{
/*
conn.resize(6);
conn[0] = this->node(0);
conn[1] = this->node(2);
conn[2] = this->node(1);
conn[3] = this->node(3);
conn[4] = this->node(5);
conn[5] = this->node(4);
*/
// VTK's VTK_QUADRATIC_WEDGE first 9 nodes match, then their
// middle and top layers of mid-edge nodes are reversed from
// LibMesh's.
conn.resize(15);
for (unsigned i=0; i<9; ++i)
conn[i] = this->node(i);
// top "ring" of mid-edge nodes
conn[9] = this->node(12);
conn[10] = this->node(13);
conn[11] = this->node(14);
// middle "ring" of mid-edge nodes
conn[12] = this->node(9);
conn[13] = this->node(10);
conn[14] = this->node(11);
return;
}
default:
libmesh_error();
}
libmesh_error();
}
// ------------------------------------------------------------
// MetisPartitioner implementation
void MetisPartitioner::_do_partition (MeshBase & mesh,
const unsigned int n_pieces)
{
libmesh_assert_greater (n_pieces, 0);
libmesh_assert (mesh.is_serial());
// Check for an easy return
if (n_pieces == 1)
{
this->single_partition (mesh);
return;
}
// What to do if the Metis library IS NOT present
#ifndef LIBMESH_HAVE_METIS
libmesh_here();
libMesh::err << "ERROR: The library has been built without" << std::endl
<< "Metis support. Using a space-filling curve" << std::endl
<< "partitioner instead!" << std::endl;
SFCPartitioner sfcp;
sfcp.partition (mesh, n_pieces);
// What to do if the Metis library IS present
#else
LOG_SCOPE("partition()", "MetisPartitioner");
const dof_id_type n_active_elem = mesh.n_active_elem();
// build the graph
// std::vector<Metis::idx_t> options(5);
std::vector<Metis::idx_t> vwgt(n_active_elem);
std::vector<Metis::idx_t> part(n_active_elem);
Metis::idx_t
n = static_cast<Metis::idx_t>(n_active_elem), // number of "nodes" (elements)
// in the graph
// wgtflag = 2, // weights on vertices only,
// // none on edges
// numflag = 0, // C-style 0-based numbering
nparts = static_cast<Metis::idx_t>(n_pieces), // number of subdomains to create
edgecut = 0; // the numbers of edges cut by the
// resulting partition
// Set the options
// options[0] = 0; // use default options
// Metis will only consider the active elements.
// We need to map the active element ids into a
// contiguous range. Further, we want the unique range indexing to be
// independent of the element ordering, otherwise a circular dependency
// can result in which the partitioning depends on the ordering which
// depends on the partitioning...
vectormap<dof_id_type, dof_id_type> global_index_map;
global_index_map.reserve (n_active_elem);
{
std::vector<dof_id_type> global_index;
MeshBase::element_iterator it = mesh.active_elements_begin();
const MeshBase::element_iterator end = mesh.active_elements_end();
MeshCommunication().find_global_indices (mesh.comm(),
MeshTools::bounding_box(mesh),
it, end, global_index);
libmesh_assert_equal_to (global_index.size(), n_active_elem);
for (std::size_t cnt=0; it != end; ++it)
{
const Elem * elem = *it;
global_index_map.insert (std::make_pair(elem->id(), global_index[cnt++]));
}
libmesh_assert_equal_to (global_index_map.size(), n_active_elem);
}
// If we have boundary elements in this mesh, we want to account for
// the connectivity between them and interior elements. We can find
// interior elements from boundary elements, but we need to build up
// a lookup map to do the reverse.
typedef LIBMESH_BEST_UNORDERED_MULTIMAP<const Elem *, const Elem *>
map_type;
map_type interior_to_boundary_map;
{
MeshBase::const_element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::const_element_iterator elem_end = mesh.active_elements_end();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
// If we don't have an interior_parent then there's nothing to look us
// up.
if ((elem->dim() >= LIBMESH_DIM) ||
!elem->interior_parent())
continue;
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
// FIXME - non-const versions of the Elem set methods
// would be nice
Elem * neighbor = const_cast<Elem *>(*n_it);
#if defined(LIBMESH_HAVE_UNORDERED_MULTIMAP) || \
defined(LIBMESH_HAVE_TR1_UNORDERED_MULTIMAP) || \
defined(LIBMESH_HAVE_HASH_MULTIMAP) || \
defined(LIBMESH_HAVE_EXT_HASH_MULTIMAP)
interior_to_boundary_map.insert
(std::make_pair(neighbor, elem));
#else
interior_to_boundary_map.insert
(interior_to_boundary_map.begin(),
std::make_pair(neighbor, elem));
#endif
}
}
}
// Invoke METIS, but only on processor 0.
// Then broadcast the resulting decomposition
if (mesh.processor_id() == 0)
{
METIS_CSR_Graph<Metis::idx_t> csr_graph;
csr_graph.offsets.resize(n_active_elem+1, 0);
// Local scope for these
{
// build the graph in CSR format. Note that
// the edges in the graph will correspond to
// face neighbors
#ifdef LIBMESH_ENABLE_AMR
std::vector<const Elem *> neighbors_offspring;
#endif
MeshBase::element_iterator elem_it = mesh.active_elements_begin();
const MeshBase::element_iterator elem_end = mesh.active_elements_end();
#ifndef NDEBUG
std::size_t graph_size=0;
#endif
// (1) first pass - get the row sizes for each element by counting the number
// of face neighbors. Also populate the vwght array if necessary
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
const dof_id_type elem_global_index =
global_index_map[elem->id()];
libmesh_assert_less (elem_global_index, vwgt.size());
// maybe there is a better weight?
// The weight is used to define what a balanced graph is
if(!_weights)
vwgt[elem_global_index] = elem->n_nodes();
else
vwgt[elem_global_index] = static_cast<Metis::idx_t>((*_weights)[elem->id()]);
unsigned int num_neighbors = 0;
// Loop over the element's neighbors. An element
// adjacency corresponds to a face neighbor
for (unsigned int ms=0; ms<elem->n_neighbors(); ms++)
{
const Elem * neighbor = elem->neighbor(ms);
if (neighbor != libmesh_nullptr)
{
// If the neighbor is active treat it
// as a connection
if (neighbor->active())
num_neighbors++;
#ifdef LIBMESH_ENABLE_AMR
// Otherwise we need to find all of the
// neighbor's children that are connected to
// us and add them
else
{
// The side of the neighbor to which
// we are connected
const unsigned int ns =
neighbor->which_neighbor_am_i (elem);
libmesh_assert_less (ns, neighbor->n_neighbors());
// Get all the active children (& grandchildren, etc...)
// of the neighbor.
// FIXME - this is the wrong thing, since we
// should be getting the active family tree on
// our side only. But adding too many graph
// links may cause hanging nodes to tend to be
// on partition interiors, which would reduce
// communication overhead for constraint
// equations, so we'll leave it.
neighbor->active_family_tree (neighbors_offspring);
// Get all the neighbor's children that
// live on that side and are thus connected
// to us
for (unsigned int nc=0; nc<neighbors_offspring.size(); nc++)
{
const Elem * child =
neighbors_offspring[nc];
// This does not assume a level-1 mesh.
// Note that since children have sides numbered
// coincident with the parent then this is a sufficient test.
if (child->neighbor(ns) == elem)
{
libmesh_assert (child->active());
num_neighbors++;
}
}
}
#endif /* ifdef LIBMESH_ENABLE_AMR */
}
}
// Check for any interior neighbors
if ((elem->dim() < LIBMESH_DIM) &&
elem->interior_parent())
{
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
num_neighbors += neighbor_set.size();
}
// Check for any boundary neighbors
typedef map_type::iterator map_it_type;
std::pair<map_it_type, map_it_type>
bounds = interior_to_boundary_map.equal_range(elem);
num_neighbors += std::distance(bounds.first, bounds.second);
csr_graph.prep_n_nonzeros(elem_global_index, num_neighbors);
#ifndef NDEBUG
graph_size += num_neighbors;
#endif
}
csr_graph.prepare_for_use();
// (2) second pass - fill the compressed adjacency array
elem_it = mesh.active_elements_begin();
for (; elem_it != elem_end; ++elem_it)
{
const Elem * elem = *elem_it;
const dof_id_type elem_global_index =
global_index_map[elem->id()];
unsigned int connection=0;
// Loop over the element's neighbors. An element
// adjacency corresponds to a face neighbor
for (unsigned int ms=0; ms<elem->n_neighbors(); ms++)
{
const Elem * neighbor = elem->neighbor(ms);
if (neighbor != libmesh_nullptr)
{
// If the neighbor is active treat it
// as a connection
if (neighbor->active())
csr_graph(elem_global_index, connection++) = global_index_map[neighbor->id()];
#ifdef LIBMESH_ENABLE_AMR
// Otherwise we need to find all of the
// neighbor's children that are connected to
// us and add them
else
{
// The side of the neighbor to which
// we are connected
const unsigned int ns =
neighbor->which_neighbor_am_i (elem);
libmesh_assert_less (ns, neighbor->n_neighbors());
// Get all the active children (& grandchildren, etc...)
// of the neighbor.
neighbor->active_family_tree (neighbors_offspring);
// Get all the neighbor's children that
// live on that side and are thus connected
// to us
for (unsigned int nc=0; nc<neighbors_offspring.size(); nc++)
{
const Elem * child =
neighbors_offspring[nc];
// This does not assume a level-1 mesh.
// Note that since children have sides numbered
// coincident with the parent then this is a sufficient test.
if (child->neighbor(ns) == elem)
{
libmesh_assert (child->active());
csr_graph(elem_global_index, connection++) = global_index_map[child->id()];
}
}
}
#endif /* ifdef LIBMESH_ENABLE_AMR */
}
}
if ((elem->dim() < LIBMESH_DIM) &&
elem->interior_parent())
{
// get all relevant interior elements
std::set<const Elem *> neighbor_set;
elem->find_interior_neighbors(neighbor_set);
std::set<const Elem *>::iterator n_it = neighbor_set.begin();
for (; n_it != neighbor_set.end(); ++n_it)
{
// FIXME - non-const versions of the Elem set methods
// would be nice
Elem * neighbor = const_cast<Elem *>(*n_it);
csr_graph(elem_global_index, connection++) =
global_index_map[neighbor->id()];
}
}
// Check for any boundary neighbors
typedef map_type::iterator map_it_type;
std::pair<map_it_type, map_it_type>
bounds = interior_to_boundary_map.equal_range(elem);
for (map_it_type it = bounds.first; it != bounds.second; ++it)
{
const Elem * neighbor = it->second;
csr_graph(elem_global_index, connection++) =
global_index_map[neighbor->id()];
}
}
// We create a non-empty vals for a disconnected graph, to
// work around a segfault from METIS.
libmesh_assert_equal_to (csr_graph.vals.size(),
std::max(graph_size,std::size_t(1)));
} // done building the graph
Metis::idx_t ncon = 1;
// Select which type of partitioning to create
// Use recursive if the number of partitions is less than or equal to 8
if (n_pieces <= 8)
Metis::METIS_PartGraphRecursive(&n, &ncon, &csr_graph.offsets[0], &csr_graph.vals[0], &vwgt[0], libmesh_nullptr,
libmesh_nullptr, &nparts, libmesh_nullptr, libmesh_nullptr, libmesh_nullptr,
&edgecut, &part[0]);
// Otherwise use kway
else
Metis::METIS_PartGraphKway(&n, &ncon, &csr_graph.offsets[0], &csr_graph.vals[0], &vwgt[0], libmesh_nullptr,
libmesh_nullptr, &nparts, libmesh_nullptr, libmesh_nullptr, libmesh_nullptr,
&edgecut, &part[0]);
} // end processor 0 part
// Broadcase the resutling partition
mesh.comm().broadcast(part);
// Assign the returned processor ids. The part array contains
// the processor id for each active element, but in terms of
// the contiguous indexing we defined above
{
MeshBase::element_iterator it = mesh.active_elements_begin();
const MeshBase::element_iterator end = mesh.active_elements_end();
for (; it!=end; ++it)
{
Elem * elem = *it;
libmesh_assert (global_index_map.count(elem->id()));
const dof_id_type elem_global_index =
global_index_map[elem->id()];
libmesh_assert_less (elem_global_index, part.size());
const processor_id_type elem_procid =
static_cast<processor_id_type>(part[elem_global_index]);
elem->processor_id() = elem_procid;
}
}
#endif
}
Real FE<3,HERMITE>::shape_second_deriv(const Elem* elem,
const Order order,
const unsigned int i,
const unsigned int j,
const Point& p)
{
libmesh_assert(elem);
hermite_compute_coefs(elem);
#ifdef LIBMESH_HAVE_TBB_API
std::vector<std::vector<Real> > & dxdxi = dxdxi_tls.local();
#endif
const ElemType type = elem->type();
const Order totalorder = static_cast<Order>(order + elem->p_level());
switch (totalorder)
{
// 3rd-order tricubic Hermite functions
case THIRD:
{
switch (type)
{
case HEX8:
case HEX20:
case HEX27:
{
libmesh_assert_less (i, 64);
std::vector<unsigned int> bases1D;
Real coef = hermite_bases_3D(bases1D, dxdxi, totalorder, i);
switch (j) // Derivative type
{
case 0:
return coef *
FEHermite<1>::hermite_raw_shape_second_deriv(bases1D[0],p(0)) *
FEHermite<1>::hermite_raw_shape(bases1D[1],p(1)) *
FEHermite<1>::hermite_raw_shape(bases1D[2],p(2));
break;
case 1:
return coef *
FEHermite<1>::hermite_raw_shape_deriv(bases1D[0],p(0)) *
FEHermite<1>::hermite_raw_shape_deriv(bases1D[1],p(1)) *
FEHermite<1>::hermite_raw_shape(bases1D[2],p(2));
break;
case 2:
return coef *
FEHermite<1>::hermite_raw_shape(bases1D[0],p(0)) *
FEHermite<1>::hermite_raw_shape_second_deriv(bases1D[1],p(1)) *
FEHermite<1>::hermite_raw_shape(bases1D[2],p(2));
break;
case 3:
return coef *
FEHermite<1>::hermite_raw_shape_deriv(bases1D[0],p(0)) *
FEHermite<1>::hermite_raw_shape(bases1D[1],p(1)) *
FEHermite<1>::hermite_raw_shape_deriv(bases1D[2],p(2));
break;
case 4:
return coef *
FEHermite<1>::hermite_raw_shape(bases1D[0],p(0)) *
FEHermite<1>::hermite_raw_shape_deriv(bases1D[1],p(1)) *
FEHermite<1>::hermite_raw_shape_deriv(bases1D[2],p(2));
break;
case 5:
return coef *
FEHermite<1>::hermite_raw_shape(bases1D[0],p(0)) *
FEHermite<1>::hermite_raw_shape(bases1D[1],p(1)) *
FEHermite<1>::hermite_raw_shape_second_deriv(bases1D[2],p(2));
break;
}
}
default:
libMesh::err << "ERROR: Unsupported element type!" << std::endl;
libmesh_error();
}
}
// by default throw an error
default:
libMesh::err << "ERROR: Unsupported polynomial order!" << std::endl;
libmesh_error();
}
libmesh_error();
return 0.;
}
Real FE<2,HIERARCHIC>::shape(const Elem * elem,
const Order order,
const unsigned int i,
const Point & p)
{
libmesh_assert(elem);
const Order totalorder = static_cast<Order>(order+elem->p_level());
libmesh_assert_greater (totalorder, 0);
switch (elem->type())
{
case TRI3:
case TRISHELL3:
case TRI6:
{
const Real zeta1 = p(0);
const Real zeta2 = p(1);
const Real zeta0 = 1. - zeta1 - zeta2;
libmesh_assert_less (i, (totalorder+1u)*(totalorder+2u)/2);
libmesh_assert (elem->type() == TRI6 || totalorder < 2);
// Vertex DoFs
if (i == 0)
return zeta0;
else if (i == 1)
return zeta1;
else if (i == 2)
return zeta2;
// Edge DoFs
else if (i < totalorder + 2u)
{
// Avoid returning NaN on vertices!
if (zeta0 + zeta1 == 0.)
return 0.;
const unsigned int basisorder = i - 1;
// Get factors to account for edge-flipping
Real f0 = 1;
if (basisorder%2 && (elem->point(0) > elem->point(1)))
f0 = -1.;
Real edgeval = (zeta1 - zeta0) / (zeta1 + zeta0);
Real crossfunc = zeta0 + zeta1;
for (unsigned int n=1; n != basisorder; ++n)
crossfunc *= (zeta0 + zeta1);
return f0 * crossfunc *
FE<1,HIERARCHIC>::shape(EDGE3, totalorder,
basisorder, edgeval);
}
else if (i < 2u*totalorder + 1)
{
// Avoid returning NaN on vertices!
if (zeta1 + zeta2 == 0.)
return 0.;
const unsigned int basisorder = i - totalorder;
// Get factors to account for edge-flipping
Real f1 = 1;
if (basisorder%2 && (elem->point(1) > elem->point(2)))
f1 = -1.;
Real edgeval = (zeta2 - zeta1) / (zeta2 + zeta1);
Real crossfunc = zeta2 + zeta1;
for (unsigned int n=1; n != basisorder; ++n)
crossfunc *= (zeta2 + zeta1);
return f1 * crossfunc *
FE<1,HIERARCHIC>::shape(EDGE3, totalorder,
basisorder, edgeval);
}
else if (i < 3u*totalorder)
{
// Avoid returning NaN on vertices!
if (zeta0 + zeta2 == 0.)
return 0.;
const unsigned int basisorder = i - (2u*totalorder) + 1;
// Get factors to account for edge-flipping
Real f2 = 1;
if (basisorder%2 && (elem->point(2) > elem->point(0)))
f2 = -1.;
Real edgeval = (zeta0 - zeta2) / (zeta0 + zeta2);
Real crossfunc = zeta0 + zeta2;
for (unsigned int n=1; n != basisorder; ++n)
crossfunc *= (zeta0 + zeta2);
return f2 * crossfunc *
FE<1,HIERARCHIC>::shape(EDGE3, totalorder,
basisorder, edgeval);
}
// Interior DoFs
else
{
const unsigned int basisnum = i - (3u*totalorder);
unsigned int exp0 = triangular_number_column[basisnum] + 1;
unsigned int exp1 = triangular_number_row[basisnum] + 1 -
triangular_number_column[basisnum];
Real returnval = 1;
for (unsigned int n = 0; n != exp0; ++n)
returnval *= zeta0;
for (unsigned int n = 0; n != exp1; ++n)
returnval *= zeta1;
returnval *= zeta2;
return returnval;
}
}
// Hierarchic shape functions on the quadrilateral.
case QUAD4:
case QUADSHELL4:
libmesh_assert_less (totalorder, 2);
libmesh_fallthrough();
case QUAD8:
case QUADSHELL8:
case QUAD9:
{
// Compute quad shape functions as a tensor-product
const Real xi = p(0);
const Real eta = p(1);
libmesh_assert_less (i, (totalorder+1u)*(totalorder+1u));
// Example i, i0, i1 values for totalorder = 5:
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
// static const unsigned int i0[] = {0, 1, 1, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 0, 0, 0, 0, 2, 3, 3, 2, 4, 4, 4, 3, 2, 5, 5, 5, 5, 4, 3, 2};
// static const unsigned int i1[] = {0, 0, 1, 1, 0, 0, 0, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 2, 2, 3, 3, 2, 3, 4, 4, 4, 2, 3, 4, 5, 5, 5, 5};
unsigned int i0, i1;
// Vertex DoFs
if (i == 0)
{ i0 = 0; i1 = 0; }
else if (i == 1)
{ i0 = 1; i1 = 0; }
else if (i == 2)
{ i0 = 1; i1 = 1; }
else if (i == 3)
{ i0 = 0; i1 = 1; }
// Edge DoFs
else if (i < totalorder + 3u)
{ i0 = i - 2; i1 = 0; }
else if (i < 2u*totalorder + 2)
{ i0 = 1; i1 = i - totalorder - 1; }
else if (i < 3u*totalorder + 1)
{ i0 = i - 2u*totalorder; i1 = 1; }
else if (i < 4u*totalorder)
{ i0 = 0; i1 = i - 3u*totalorder + 1; }
// Interior DoFs
else
{
unsigned int basisnum = i - 4*totalorder;
i0 = square_number_column[basisnum] + 2;
i1 = square_number_row[basisnum] + 2;
}
// Flip odd degree of freedom values if necessary
// to keep continuity on sides
Real f = 1.;
if ((i0%2) && (i0 > 2) && (i1 == 0))
f = (elem->point(0) > elem->point(1))?-1.:1.;
else if ((i0%2) && (i0>2) && (i1 == 1))
f = (elem->point(3) > elem->point(2))?-1.:1.;
else if ((i0 == 0) && (i1%2) && (i1>2))
f = (elem->point(0) > elem->point(3))?-1.:1.;
else if ((i0 == 1) && (i1%2) && (i1>2))
f = (elem->point(1) > elem->point(2))?-1.:1.;
return f*(FE<1,HIERARCHIC>::shape(EDGE3, totalorder, i0, xi)*
FE<1,HIERARCHIC>::shape(EDGE3, totalorder, i1, eta));
}
default:
libmesh_error_msg("ERROR: Unsupported element type = " << elem->type());
}
return 0.;
}
Real FE<2,HIERARCHIC>::shape_deriv(const Elem * elem,
const Order order,
const unsigned int i,
const unsigned int j,
const Point & p)
{
libmesh_assert(elem);
const ElemType type = elem->type();
const Order totalorder = static_cast<Order>(order+elem->p_level());
libmesh_assert_greater (totalorder, 0);
switch (type)
{
// 1st & 2nd-order Hierarchics.
case TRI3:
case TRISHELL3:
case TRI6:
{
const Real eps = 1.e-6;
libmesh_assert_less (j, 2);
switch (j)
{
// d()/dxi
case 0:
{
const Point pp(p(0)+eps, p(1));
const Point pm(p(0)-eps, p(1));
return (FE<2,HIERARCHIC>::shape(elem, order, i, pp) -
FE<2,HIERARCHIC>::shape(elem, order, i, pm))/2./eps;
}
// d()/deta
case 1:
{
const Point pp(p(0), p(1)+eps);
const Point pm(p(0), p(1)-eps);
return (FE<2,HIERARCHIC>::shape(elem, order, i, pp) -
FE<2,HIERARCHIC>::shape(elem, order, i, pm))/2./eps;
}
default:
libmesh_error_msg("Invalid derivative index j = " << j);
}
}
case QUAD4:
case QUADSHELL4:
libmesh_assert_less (totalorder, 2);
libmesh_fallthrough();
case QUAD8:
case QUADSHELL8:
case QUAD9:
{
// Compute quad shape functions as a tensor-product
const Real xi = p(0);
const Real eta = p(1);
libmesh_assert_less (i, (totalorder+1u)*(totalorder+1u));
// Example i, i0, i1 values for totalorder = 5:
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
// static const unsigned int i0[] = {0, 1, 1, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 0, 0, 0, 0, 2, 3, 4, 5, 2, 3, 4, 5, 2, 3, 4, 5, 2, 3, 4, 5};
// static const unsigned int i1[] = {0, 0, 1, 1, 0, 0, 0, 0, 2, 3, 4, 5, 1, 1, 1, 1, 2, 3, 4, 5, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5};
unsigned int i0, i1;
// Vertex DoFs
if (i == 0)
{ i0 = 0; i1 = 0; }
else if (i == 1)
{ i0 = 1; i1 = 0; }
else if (i == 2)
{ i0 = 1; i1 = 1; }
else if (i == 3)
{ i0 = 0; i1 = 1; }
// Edge DoFs
else if (i < totalorder + 3u)
{ i0 = i - 2; i1 = 0; }
else if (i < 2u*totalorder + 2)
{ i0 = 1; i1 = i - totalorder - 1; }
else if (i < 3u*totalorder + 1u)
{ i0 = i - 2u*totalorder; i1 = 1; }
else if (i < 4u*totalorder)
{ i0 = 0; i1 = i - 3u*totalorder + 1; }
// Interior DoFs
else
{
unsigned int basisnum = i - 4*totalorder;
i0 = square_number_column[basisnum] + 2;
i1 = square_number_row[basisnum] + 2;
}
// Flip odd degree of freedom values if necessary
// to keep continuity on sides
Real f = 1.;
if ((i0%2) && (i0 > 2) && (i1 == 0))
f = (elem->point(0) > elem->point(1))?-1.:1.;
else if ((i0%2) && (i0>2) && (i1 == 1))
f = (elem->point(3) > elem->point(2))?-1.:1.;
else if ((i0 == 0) && (i1%2) && (i1>2))
f = (elem->point(0) > elem->point(3))?-1.:1.;
else if ((i0 == 1) && (i1%2) && (i1>2))
f = (elem->point(1) > elem->point(2))?-1.:1.;
switch (j)
{
// d()/dxi
case 0:
return f*(FE<1,HIERARCHIC>::shape_deriv(EDGE3, totalorder, i0, 0, xi)*
FE<1,HIERARCHIC>::shape (EDGE3, totalorder, i1, eta));
// d()/deta
case 1:
return f*(FE<1,HIERARCHIC>::shape (EDGE3, totalorder, i0, xi)*
FE<1,HIERARCHIC>::shape_deriv(EDGE3, totalorder, i1, 0, eta));
default:
libmesh_error_msg("Invalid derivative index j = " << j);
}
}
default:
libmesh_error_msg("ERROR: Unsupported element type = " << type);
}
return 0.;
}
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);
}
}
UniquePtr<Elem> InfHex16::build_side (const unsigned int i,
bool proxy) const
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
switch (i)
{
// base
case 0:
return UniquePtr<Elem>(new Side<Quad8,InfHex16>(this,i));
// ifem sides
case 1:
case 2:
case 3:
case 4:
return UniquePtr<Elem>(new Side<InfQuad6,InfHex16>(this,i));
default:
libmesh_error_msg("Invalid side i = " << i);
}
}
else
{
// Create NULL pointer to be initialized, returned later.
Elem* face = NULL;
// Think of a unit cube: (-1,1) x (-1,1) x (1,1)
switch (i)
{
case 0: // the base face
{
face = new Quad8;
// Only here, the face element's normal points inward
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(2);
face->set_node(3) = this->get_node(3);
face->set_node(4) = this->get_node(8);
face->set_node(5) = this->get_node(9);
face->set_node(6) = this->get_node(10);
face->set_node(7) = this->get_node(11);
break;
}
case 1: // connecting to another infinite element
{
face = new InfQuad6;
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(4);
face->set_node(3) = this->get_node(5);
face->set_node(4) = this->get_node(8);
face->set_node(5) = this->get_node(12);
break;
}
case 2: // connecting to another infinite element
{
face = new InfQuad6;
face->set_node(0) = this->get_node(1);
face->set_node(1) = this->get_node(2);
face->set_node(2) = this->get_node(5);
face->set_node(3) = this->get_node(6);
face->set_node(4) = this->get_node(9);
face->set_node(5) = this->get_node(13);
break;
}
case 3: // connecting to another infinite element
{
face = new InfQuad6;
face->set_node(0) = this->get_node(2);
face->set_node(1) = this->get_node(3);
face->set_node(2) = this->get_node(6);
face->set_node(3) = this->get_node(7);
face->set_node(4) = this->get_node(10);
face->set_node(5) = this->get_node(14);
break;
}
case 4: // connecting to another infinite element
{
face = new InfQuad6;
face->set_node(0) = this->get_node(3);
face->set_node(1) = this->get_node(0);
face->set_node(2) = this->get_node(7);
face->set_node(3) = this->get_node(4);
face->set_node(4) = this->get_node(11);
face->set_node(5) = this->get_node(15);
break;
}
default:
libmesh_error_msg("Invalid side i = " << i);
}
face->subdomain_id() = this->subdomain_id();
return UniquePtr<Elem>(face);
}
libmesh_error_msg("We'll never get here!");
return UniquePtr<Elem>();
}
NumericVector<Number>& RBEvaluation::get_basis_function(unsigned int i)
{
libmesh_assert_less (i, basis_functions.size());
return *(basis_functions[i]);
}
void Tri6::connectivity(const unsigned int sf,
const IOPackage iop,
std::vector<dof_id_type>& conn) const
{
libmesh_assert_less (sf, this->n_sub_elem());
libmesh_assert_not_equal_to (iop, INVALID_IO_PACKAGE);
switch (iop)
{
case TECPLOT:
{
conn.resize(4);
switch(sf)
{
case 0:
// linear sub-triangle 0
conn[0] = this->node(0)+1;
conn[1] = this->node(3)+1;
conn[2] = this->node(5)+1;
conn[3] = this->node(5)+1;
return;
case 1:
// linear sub-triangle 1
conn[0] = this->node(3)+1;
conn[1] = this->node(1)+1;
conn[2] = this->node(4)+1;
conn[3] = this->node(4)+1;
return;
case 2:
// linear sub-triangle 2
conn[0] = this->node(5)+1;
conn[1] = this->node(4)+1;
conn[2] = this->node(2)+1;
conn[3] = this->node(2)+1;
return;
case 3:
// linear sub-triangle 3
conn[0] = this->node(3)+1;
conn[1] = this->node(4)+1;
conn[2] = this->node(5)+1;
conn[3] = this->node(5)+1;
return;
default:
libmesh_error_msg("Invalid sf = " << sf);
}
}
case VTK:
{
// VTK_QUADRATIC_TRIANGLE has same numbering as libmesh TRI6
conn.resize(6);
conn[0] = this->node(0);
conn[1] = this->node(1);
conn[2] = this->node(2);
conn[3] = this->node(3);
conn[4] = this->node(4);
conn[5] = this->node(5);
return;
// Used to write out linear sub-triangles for VTK...
/*
conn.resize(3);
switch(sf)
{
case 0:
// linear sub-triangle 0
conn[0] = this->node(0);
conn[1] = this->node(3);
conn[2] = this->node(5);
return;
case 1:
// linear sub-triangle 1
conn[0] = this->node(3);
conn[1] = this->node(1);
conn[2] = this->node(4);
return;
case 2:
// linear sub-triangle 2
conn[0] = this->node(5);
conn[1] = this->node(4);
conn[2] = this->node(2);
return;
case 3:
// linear sub-triangle 3
conn[0] = this->node(3);
conn[1] = this->node(4);
conn[2] = this->node(5);
return;
default:
libmesh_error_msg("Invalid sf = " << sf);
}
*/
}
default:
libmesh_error_msg("Unsupported IO package " << iop);
}
}
std::string AntiochChemistry::species_name( unsigned int species_index ) const
{
libmesh_assert_less(species_index, _antioch_gas->n_species());
return _antioch_gas->species_inverse_name_map().find(species_index)->second;
}
AutoPtr<Elem> Tet10::build_edge (const unsigned int i) const
{
libmesh_assert_less (i, this->n_edges());
return AutoPtr<Elem>(new SideEdge<Edge3,Tet10>(this,i));
}
void Partitioner::partition_unpartitioned_elements (MeshBase & mesh,
const unsigned int n_subdomains)
{
MeshBase::element_iterator it = mesh.unpartitioned_elements_begin();
const MeshBase::element_iterator end = mesh.unpartitioned_elements_end();
const dof_id_type n_unpartitioned_elements = MeshTools::n_elem (it, end);
// the unpartitioned elements must exist on all processors. If the range is empty on one
// it is empty on all, and we can quit right here.
if (!n_unpartitioned_elements) return;
// find the target subdomain sizes
std::vector<dof_id_type> subdomain_bounds(mesh.n_processors());
for (processor_id_type pid=0; pid<mesh.n_processors(); pid++)
{
dof_id_type tgt_subdomain_size = 0;
// watch out for the case that n_subdomains < n_processors
if (pid < n_subdomains)
{
tgt_subdomain_size = n_unpartitioned_elements/n_subdomains;
if (pid < n_unpartitioned_elements%n_subdomains)
tgt_subdomain_size++;
}
//libMesh::out << "pid, #= " << pid << ", " << tgt_subdomain_size << std::endl;
if (pid == 0)
subdomain_bounds[0] = tgt_subdomain_size;
else
subdomain_bounds[pid] = subdomain_bounds[pid-1] + tgt_subdomain_size;
}
libmesh_assert_equal_to (subdomain_bounds.back(), n_unpartitioned_elements);
// create the unique mapping for all unpartitioned elements independent of partitioning
// determine the global indexing for all the unpartitioned elements
std::vector<dof_id_type> global_indices;
// Calling this on all processors a unique range in [0,n_unpartitioned_elements) is constructed.
// Only the indices for the elements we pass in are returned in the array.
MeshCommunication().find_global_indices (mesh.comm(),
MeshTools::create_bounding_box(mesh), it, end,
global_indices);
for (dof_id_type cnt=0; it != end; ++it)
{
Elem * elem = *it;
libmesh_assert_less (cnt, global_indices.size());
const dof_id_type global_index =
global_indices[cnt++];
libmesh_assert_less (global_index, subdomain_bounds.back());
libmesh_assert_less (global_index, n_unpartitioned_elements);
const processor_id_type subdomain_id =
cast_int<processor_id_type>
(std::distance(subdomain_bounds.begin(),
std::upper_bound(subdomain_bounds.begin(),
subdomain_bounds.end(),
global_index)));
libmesh_assert_less (subdomain_id, n_subdomains);
elem->processor_id() = subdomain_id;
//libMesh::out << "assigning " << global_index << " to " << subdomain_id << std::endl;
}
}
AutoPtr<Elem> InfHex18::build_side (const unsigned int i,
bool proxy) const
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
switch (i)
{
// base
case 0:
{
AutoPtr<Elem> ap(new Side<Quad9,InfHex18>(this,i));
return ap;
}
// ifem sides
case 1:
case 2:
case 3:
case 4:
{
AutoPtr<Elem> ap(new Side<InfQuad6,InfHex18>(this,i));
return ap;
}
default:
libmesh_error_msg("Invalid side i = " << i);
}
}
else
{
// Create NULL pointer to be initialized, returned later.
AutoPtr<Elem> face(NULL);
// Think of a unit cube: (-1,1) x (-1,1) x (1,1)
switch (i)
{
case 0: // the base face
{
face.reset(new Quad9);
// This is the exception: all other face elements' normals
// point outwards; but the base element's normal points inward
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(2);
face->set_node(3) = this->get_node(3);
face->set_node(4) = this->get_node(8);
face->set_node(5) = this->get_node(9);
face->set_node(6) = this->get_node(10);
face->set_node(7) = this->get_node(11);
face->set_node(8) = this->get_node(16);
break;
}
case 1: // connecting to another infinite element
{
face.reset(new InfQuad6);
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(4);
face->set_node(3) = this->get_node(5);
face->set_node(4) = this->get_node(8);
face->set_node(5) = this->get_node(12);
break;
}
case 2: // connecting to another infinite element
{
face.reset(new InfQuad6);
face->set_node(0) = this->get_node(1);
face->set_node(1) = this->get_node(2);
face->set_node(2) = this->get_node(5);
face->set_node(3) = this->get_node(6);
face->set_node(4) = this->get_node(9);
face->set_node(5) = this->get_node(13);
break;
}
case 3: // connecting to another infinite element
{
face.reset(new InfQuad6);
face->set_node(0) = this->get_node(2);
face->set_node(1) = this->get_node(3);
face->set_node(2) = this->get_node(6);
face->set_node(3) = this->get_node(7);
face->set_node(4) = this->get_node(10);
face->set_node(5) = this->get_node(14);
break;
}
case 4: // connecting to another infinite element
{
face.reset(new InfQuad6);
face->set_node(0) = this->get_node(3);
face->set_node(1) = this->get_node(0);
face->set_node(2) = this->get_node(7);
face->set_node(3) = this->get_node(4);
face->set_node(4) = this->get_node(11);
face->set_node(5) = this->get_node(15);
break;
}
default:
libmesh_error_msg("Invalid side i = " << i);
}
face->subdomain_id() = this->subdomain_id();
return face;
}
libmesh_error_msg("We'll never get here!");
AutoPtr<Elem> ap(NULL);
return ap;
}
void Partitioner::set_parent_processor_ids(MeshBase & mesh)
{
// Ignore the parameter when !LIBMESH_ENABLE_AMR
libmesh_ignore(mesh);
LOG_SCOPE("set_parent_processor_ids()", "Partitioner");
#ifdef LIBMESH_ENABLE_AMR
// If the mesh is serial we have access to all the elements,
// in particular all the active ones. We can therefore set
// the parent processor ids indirectly through their children, and
// set the subactive processor ids while examining their active
// ancestors.
// By convention a parent is assigned to the minimum processor
// of all its children, and a subactive is assigned to the processor
// of its active ancestor.
if (mesh.is_serial())
{
for (auto & child : mesh.active_element_ptr_range())
{
// First set descendents
std::vector<const Elem *> subactive_family;
child->total_family_tree(subactive_family);
for (std::size_t i = 0; i != subactive_family.size(); ++i)
const_cast<Elem *>(subactive_family[i])->processor_id() = child->processor_id();
// Then set ancestors
Elem * parent = child->parent();
while (parent)
{
// invalidate the parent id, otherwise the min below
// will not work if the current parent id is less
// than all the children!
parent->invalidate_processor_id();
for (auto & child : parent->child_ref_range())
{
libmesh_assert(!child.is_remote());
libmesh_assert_not_equal_to (child.processor_id(), DofObject::invalid_processor_id);
parent->processor_id() = std::min(parent->processor_id(),
child.processor_id());
}
parent = parent->parent();
}
}
}
// When the mesh is parallel we cannot guarantee that parents have access to
// all their children.
else
{
// Setting subactive processor ids is easy: we can guarantee
// that children have access to all their parents.
// Loop over all the active elements in the mesh
for (auto & child : mesh.active_element_ptr_range())
{
std::vector<const Elem *> subactive_family;
child->total_family_tree(subactive_family);
for (std::size_t i = 0; i != subactive_family.size(); ++i)
const_cast<Elem *>(subactive_family[i])->processor_id() = child->processor_id();
}
// When the mesh is parallel we cannot guarantee that parents have access to
// all their children.
// We will use a brute-force approach here. Each processor finds its parent
// elements and sets the parent pid to the minimum of its
// semilocal descendants.
// A global reduction is then performed to make sure the true minimum is found.
// As noted, this is required because we cannot guarantee that a parent has
// access to all its children on any single processor.
libmesh_parallel_only(mesh.comm());
libmesh_assert(MeshTools::n_elem(mesh.unpartitioned_elements_begin(),
mesh.unpartitioned_elements_end()) == 0);
const dof_id_type max_elem_id = mesh.max_elem_id();
std::vector<processor_id_type>
parent_processor_ids (std::min(communication_blocksize,
max_elem_id));
for (dof_id_type blk=0, last_elem_id=0; last_elem_id<max_elem_id; blk++)
{
last_elem_id =
std::min(static_cast<dof_id_type>((blk+1)*communication_blocksize),
max_elem_id);
const dof_id_type first_elem_id = blk*communication_blocksize;
std::fill (parent_processor_ids.begin(),
parent_processor_ids.end(),
DofObject::invalid_processor_id);
// first build up local contributions to parent_processor_ids
MeshBase::element_iterator not_it = mesh.ancestor_elements_begin();
const MeshBase::element_iterator not_end = mesh.ancestor_elements_end();
bool have_parent_in_block = false;
for ( ; not_it != not_end; ++not_it)
{
Elem * parent = *not_it;
const dof_id_type parent_idx = parent->id();
libmesh_assert_less (parent_idx, max_elem_id);
if ((parent_idx >= first_elem_id) &&
(parent_idx < last_elem_id))
{
have_parent_in_block = true;
processor_id_type parent_pid = DofObject::invalid_processor_id;
std::vector<const Elem *> active_family;
parent->active_family_tree(active_family);
for (std::size_t i = 0; i != active_family.size(); ++i)
parent_pid = std::min (parent_pid, active_family[i]->processor_id());
const dof_id_type packed_idx = parent_idx - first_elem_id;
libmesh_assert_less (packed_idx, parent_processor_ids.size());
parent_processor_ids[packed_idx] = parent_pid;
}
}
// then find the global minimum
mesh.comm().min (parent_processor_ids);
// and assign the ids, if we have a parent in this block.
if (have_parent_in_block)
for (not_it = mesh.ancestor_elements_begin();
not_it != not_end; ++not_it)
{
Elem * parent = *not_it;
const dof_id_type parent_idx = parent->id();
if ((parent_idx >= first_elem_id) &&
(parent_idx < last_elem_id))
{
const dof_id_type packed_idx = parent_idx - first_elem_id;
libmesh_assert_less (packed_idx, parent_processor_ids.size());
const processor_id_type parent_pid =
parent_processor_ids[packed_idx];
libmesh_assert_not_equal_to (parent_pid, DofObject::invalid_processor_id);
parent->processor_id() = parent_pid;
}
}
}
}
#endif // LIBMESH_ENABLE_AMR
}
UniquePtr<Elem> InfPrism12::build_side_ptr (const unsigned int i,
bool proxy)
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
switch (i)
{
// base
case 0:
return UniquePtr<Elem>(new Side<Tri6,InfPrism12>(this,i));
// ifem sides
case 1:
case 2:
case 3:
return UniquePtr<Elem>(new Side<InfQuad6,InfPrism12>(this,i));
default:
libmesh_error_msg("Invalid side i = " << i);
}
}
else
{
// Create NULL pointer to be initialized, returned later.
Elem * face = libmesh_nullptr;
switch (i)
{
case 0: // the triangular face at z=-1, base face
{
face = new Tri6;
break;
}
case 1: // the quad face at y=0
case 2: // the other quad face
case 3: // the quad face at x=0
{
face = new InfQuad6;
break;
}
default:
libmesh_error_msg("Invalid side i = " << i);
}
face->subdomain_id() = this->subdomain_id();
// Set the nodes
for (unsigned n=0; n<face->n_nodes(); ++n)
face->set_node(n) = this->node_ptr(InfPrism12::side_nodes_map[i][n]);
return UniquePtr<Elem>(face);
}
libmesh_error_msg("We'll never get here!");
return UniquePtr<Elem>();
}
void Partitioner::set_node_processor_ids(MeshBase & mesh)
{
LOG_SCOPE("set_node_processor_ids()","Partitioner");
// This function must be run on all processors at once
libmesh_parallel_only(mesh.comm());
// If we have any unpartitioned elements at this
// stage there is a problem
libmesh_assert (MeshTools::n_elem(mesh.unpartitioned_elements_begin(),
mesh.unpartitioned_elements_end()) == 0);
// const dof_id_type orig_n_local_nodes = mesh.n_local_nodes();
// libMesh::err << "[" << mesh.processor_id() << "]: orig_n_local_nodes="
// << orig_n_local_nodes << std::endl;
// Build up request sets. Each node is currently owned by a processor because
// it is connected to an element owned by that processor. However, during the
// repartitioning phase that element may have been assigned a new processor id, but
// it is still resident on the original processor. We need to know where to look
// for new ids before assigning new ids, otherwise we may be asking the wrong processors
// for the wrong information.
//
// The only remaining issue is what to do with unpartitioned nodes. Since they are required
// to live on all processors we can simply rely on ourselves to number them properly.
std::vector<std::vector<dof_id_type>>
requested_node_ids(mesh.n_processors());
// Loop over all the nodes, count the ones on each processor. We can skip ourself
std::vector<dof_id_type> ghost_nodes_from_proc(mesh.n_processors(), 0);
for (auto & node : mesh.node_ptr_range())
{
libmesh_assert(node);
const processor_id_type current_pid = node->processor_id();
if (current_pid != mesh.processor_id() &&
current_pid != DofObject::invalid_processor_id)
{
libmesh_assert_less (current_pid, ghost_nodes_from_proc.size());
ghost_nodes_from_proc[current_pid]++;
}
}
// We know how many objects live on each processor, so reserve()
// space for each.
for (processor_id_type pid=0; pid != mesh.n_processors(); ++pid)
requested_node_ids[pid].reserve(ghost_nodes_from_proc[pid]);
// We need to get the new pid for each node from the processor
// which *currently* owns the node. We can safely skip ourself
for (auto & node : mesh.node_ptr_range())
{
libmesh_assert(node);
const processor_id_type current_pid = node->processor_id();
if (current_pid != mesh.processor_id() &&
current_pid != DofObject::invalid_processor_id)
{
libmesh_assert_less (current_pid, requested_node_ids.size());
libmesh_assert_less (requested_node_ids[current_pid].size(),
ghost_nodes_from_proc[current_pid]);
requested_node_ids[current_pid].push_back(node->id());
}
// Unset any previously-set node processor ids
node->invalidate_processor_id();
}
// Loop over all the active elements
for (auto & elem : mesh.active_element_ptr_range())
{
libmesh_assert(elem);
libmesh_assert_not_equal_to (elem->processor_id(), DofObject::invalid_processor_id);
// For each node, set the processor ID to the min of
// its current value and this Element's processor id.
//
// TODO: we would probably get better parallel partitioning if
// we did something like "min for even numbered nodes, max for
// odd numbered". We'd need to be careful about how that would
// affect solution ordering for I/O, though.
for (unsigned int n=0; n<elem->n_nodes(); ++n)
elem->node_ptr(n)->processor_id() = std::min(elem->node_ptr(n)->processor_id(),
elem->processor_id());
}
// And loop over the subactive elements, but don't reassign
// nodes that are already active on another processor.
MeshBase::element_iterator sub_it = mesh.subactive_elements_begin();
const MeshBase::element_iterator sub_end = mesh.subactive_elements_end();
for ( ; sub_it != sub_end; ++sub_it)
{
Elem * elem = *sub_it;
libmesh_assert(elem);
libmesh_assert_not_equal_to (elem->processor_id(), DofObject::invalid_processor_id);
for (unsigned int n=0; n<elem->n_nodes(); ++n)
if (elem->node_ptr(n)->processor_id() == DofObject::invalid_processor_id)
elem->node_ptr(n)->processor_id() = elem->processor_id();
}
// Same for the inactive elements -- we will have already gotten most of these
// nodes, *except* for the case of a parent with a subset of children which are
// ghost elements. In that case some of the parent nodes will not have been
// properly handled yet
MeshBase::element_iterator not_it = mesh.not_active_elements_begin();
const MeshBase::element_iterator not_end = mesh.not_active_elements_end();
for ( ; not_it != not_end; ++not_it)
{
Elem * elem = *not_it;
libmesh_assert(elem);
libmesh_assert_not_equal_to (elem->processor_id(), DofObject::invalid_processor_id);
for (unsigned int n=0; n<elem->n_nodes(); ++n)
if (elem->node_ptr(n)->processor_id() == DofObject::invalid_processor_id)
elem->node_ptr(n)->processor_id() = elem->processor_id();
}
// We can't assert that all nodes are connected to elements, because
// a DistributedMesh with NodeConstraints might have pulled in some
// remote nodes solely for evaluating those constraints.
// MeshTools::libmesh_assert_connected_nodes(mesh);
// For such nodes, we'll do a sanity check later when making sure
// that we successfully reset their processor ids to something
// valid.
// Next set node ids from other processors, excluding self
for (processor_id_type p=1; p != mesh.n_processors(); ++p)
{
// Trade my requests with processor procup and procdown
processor_id_type procup = cast_int<processor_id_type>
((mesh.processor_id() + p) % mesh.n_processors());
processor_id_type procdown = cast_int<processor_id_type>
((mesh.n_processors() + mesh.processor_id() - p) %
mesh.n_processors());
std::vector<dof_id_type> request_to_fill;
mesh.comm().send_receive(procup, requested_node_ids[procup],
procdown, request_to_fill);
// Fill those requests in-place
for (std::size_t i=0; i != request_to_fill.size(); ++i)
{
Node & node = mesh.node_ref(request_to_fill[i]);
const processor_id_type new_pid = node.processor_id();
// We may have an invalid processor_id() on nodes that have been
// "detached" from coarsened-away elements but that have not yet
// themselves been removed.
// libmesh_assert_not_equal_to (new_pid, DofObject::invalid_processor_id);
// libmesh_assert_less (new_pid, mesh.n_partitions()); // this is the correct test --
request_to_fill[i] = new_pid; // the number of partitions may
} // not equal the number of processors
// Trade back the results
std::vector<dof_id_type> filled_request;
mesh.comm().send_receive(procdown, request_to_fill,
procup, filled_request);
libmesh_assert_equal_to (filled_request.size(), requested_node_ids[procup].size());
// And copy the id changes we've now been informed of
for (std::size_t i=0; i != filled_request.size(); ++i)
{
Node & node = mesh.node_ref(requested_node_ids[procup][i]);
// this is the correct test -- the number of partitions may
// not equal the number of processors
// But: we may have an invalid processor_id() on nodes that
// have been "detached" from coarsened-away elements but
// that have not yet themselves been removed.
// libmesh_assert_less (filled_request[i], mesh.n_partitions());
node.processor_id(cast_int<processor_id_type>(filled_request[i]));
}
}
#ifdef DEBUG
MeshTools::libmesh_assert_valid_procids<Node>(mesh);
#endif
}
AutoPtr<Elem> InfPrism12::build_side (const unsigned int i,
bool proxy) const
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
switch (i)
{
// base
case 0:
{
AutoPtr<Elem> ap(new Side<Tri6,InfPrism12>(this,i));
return ap;
}
// ifem sides
case 1:
case 2:
case 3:
{
AutoPtr<Elem> ap(new Side<InfQuad6,InfPrism12>(this,i));
return ap;
}
default:
libmesh_error();
}
}
else
{
// Create NULL pointer to be initialized, returned later.
AutoPtr<Elem> face(NULL);
switch (i)
{
case 0: // the triangular face at z=-1, base face
{
face.reset(new Tri6);
// Note that for this face element, the normal points inward
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(2);
face->set_node(3) = this->get_node(6);
face->set_node(4) = this->get_node(7);
face->set_node(5) = this->get_node(8);
break;
}
case 1: // the quad face at y=0
{
face.reset(new InfQuad6);
face->set_node(0) = this->get_node(0);
face->set_node(1) = this->get_node(1);
face->set_node(2) = this->get_node(3);
face->set_node(3) = this->get_node(4);
face->set_node(4) = this->get_node(6);
face->set_node(5) = this->get_node(9);
break;
}
case 2: // the other quad face
{
face.reset(new InfQuad6);
face->set_node(0) = this->get_node(1);
face->set_node(1) = this->get_node(2);
face->set_node(2) = this->get_node(4);
face->set_node(3) = this->get_node(5);
face->set_node(4) = this->get_node(7);
face->set_node(5) = this->get_node(10);
break;
}
case 3: // the quad face at x=0
{
face.reset(new InfQuad6);
face->set_node(0) = this->get_node(2);
face->set_node(1) = this->get_node(0);
face->set_node(2) = this->get_node(5);
face->set_node(3) = this->get_node(3);
face->set_node(4) = this->get_node(8);
face->set_node(5) = this->get_node(11);
break;
}
default:
{
libmesh_error();
}
}
face->subdomain_id() = this->subdomain_id();
return face;
}
// We'll never get here.
libmesh_error();
AutoPtr<Elem> ap(NULL); return ap;
}
AutoPtr<Elem> Quad4::build_side (const unsigned int i,
bool proxy) const
{
libmesh_assert_less (i, this->n_sides());
if (proxy)
{
AutoPtr<Elem> ap(new Side<Edge2,Quad4>(this,i));
return ap;
}
else
{
switch (i)
{
case 0:
{
Edge2* edge = new Edge2;
edge->set_node(0) = this->get_node(0);
edge->set_node(1) = this->get_node(1);
AutoPtr<Elem> ap(edge); return ap;
}
case 1:
{
Edge2* edge = new Edge2;
edge->set_node(0) = this->get_node(1);
edge->set_node(1) = this->get_node(2);
AutoPtr<Elem> ap(edge); return ap;
}
case 2:
{
Edge2* edge = new Edge2;
edge->set_node(0) = this->get_node(2);
edge->set_node(1) = this->get_node(3);
AutoPtr<Elem> ap(edge); return ap;
}
case 3:
{
Edge2* edge = new Edge2;
edge->set_node(0) = this->get_node(3);
edge->set_node(1) = this->get_node(0);
AutoPtr<Elem> ap(edge); return ap;
}
default:
{
libmesh_error();
}
}
}
// We will never get here...
AutoPtr<Elem> ap(NULL); return ap;
}
RealGradient FE<2,NEDELEC_ONE>::shape_deriv(const Elem* elem,
const Order order,
const unsigned int i,
const unsigned int j,
const Point&)
{
#if LIBMESH_DIM > 1
libmesh_assert(elem);
libmesh_assert_less (j, 2);
const Order total_order = static_cast<Order>(order + elem->p_level());
switch (total_order)
{
// linear Lagrange shape functions
case FIRST:
{
switch (elem->type())
{
case QUAD8:
case QUAD9:
{
libmesh_assert_less (i, 4);
switch (j)
{
// d()/dxi
case 0:
{
switch(i)
{
case 0:
case 2:
return RealGradient();
case 1:
{
if( elem->point(1) > elem->point(2) )
return RealGradient( 0.0, -0.25 );
else
return RealGradient( 0.0, 0.25 );
}
case 3:
{
if( elem->point(3) > elem->point(0) )
return RealGradient( 0.0, -0.25 );
else
return RealGradient( 0.0, 0.25 );
}
default:
libmesh_error();
}
} // j=0
// d()/deta
case 1:
{
switch(i)
{
case 1:
case 3:
return RealGradient();
case 0:
{
if( elem->point(0) > elem->point(1) )
return RealGradient( 0.25 );
else
return RealGradient( -0.25 );
}
case 2:
{
if( elem->point(2) > elem->point(3) )
return RealGradient( 0.25 );
else
return RealGradient( -0.25 );
}
default:
libmesh_error();
}
} // j=1
default:
libmesh_error();
}
return RealGradient();
}
case TRI6:
{
libmesh_assert_less (i, 3);
// Account for edge flipping
Real f = 1.0;
switch(i)
{
case 0:
{
if( elem->point(0) > elem->point(1) )
f = -1.0;
break;
}
case 1:
{
if( elem->point(1) > elem->point(2) )
f = -1.0;
break;
}
case 2:
{
if( elem->point(2) > elem->point(0) )
f = -1.0;
break;
}
default:
libmesh_error();
}
switch (j)
{
// d()/dxi
case 0:
{
return RealGradient( 0.0, f*1.0);
}
// d()/deta
case 1:
{
return RealGradient( f*(-1.0) );
}
default:
libmesh_error();
}
}
default:
{
libMesh::err << "ERROR: Unsupported 2D element type!: " << elem->type()
<< std::endl;
libmesh_error();
}
}
}
// unsupported order
default:
{
libMesh::err << "ERROR: Unsupported 2D FE order!: " << total_order
<< std::endl;
libmesh_error();
}
}
#endif // LIBMESH_DIM > 1
libmesh_error();
return RealGradient();
}
Real FE<2,XYZ>::shape(const Elem* elem,
const Order libmesh_dbg_var(order),
const unsigned int i,
const Point& point_in)
{
#if LIBMESH_DIM > 1
libmesh_assert(elem);
// Only recompute the centroid if the element
// has changed from the last one we computed.
// This avoids repeated centroid calculations
// when called in succession with the same element.
if (elem->id() != old_elem_id)
{
centroid = elem->centroid();
old_elem_id = elem->id();
max_distance = Point(0.,0.,0.);
for (unsigned int p = 0; p < elem->n_nodes(); p++)
for (unsigned int d = 0; d < 2; d++)
{
const Real distance = std::abs(centroid(d) - elem->point(p)(d));
max_distance(d) = std::max(distance, max_distance(d));
}
}
// Using static globals for old_elem_id, etc. will fail
// horribly with more than one thread.
libmesh_assert_equal_to (libMesh::n_threads(), 1);
const Real x = point_in(0);
const Real y = point_in(1);
const Real xc = centroid(0);
const Real yc = centroid(1);
const Real distx = max_distance(0);
const Real disty = max_distance(1);
const Real dx = (x - xc)/distx;
const Real dy = (y - yc)/disty;
#ifndef NDEBUG
// totalorder is only used in the assertion below, so
// we avoid declaring it when asserts are not active.
const unsigned int totalorder = order + elem->p_level();
#endif
libmesh_assert_less (i, (totalorder+1)*(totalorder+2)/2);
// monomials. since they are hierarchic we only need one case block.
switch (i)
{
// constant
case 0:
return 1.;
// linear
case 1:
return dx;
case 2:
return dy;
// quadratics
case 3:
return dx*dx;
case 4:
return dx*dy;
case 5:
return dy*dy;
// cubics
case 6:
return dx*dx*dx;
case 7:
return dx*dx*dy;
case 8:
return dx*dy*dy;
case 9:
return dy*dy*dy;
// quartics
case 10:
return dx*dx*dx*dx;
case 11:
return dx*dx*dx*dy;
case 12:
return dx*dx*dy*dy;
case 13:
return dx*dy*dy*dy;
case 14:
return dy*dy*dy*dy;
default:
unsigned int o = 0;
for (; i >= (o+1)*(o+2)/2; o++) { }
unsigned int i2 = i - (o*(o+1)/2);
Real val = 1.;
for (unsigned int index=i2; index != o; index++)
val *= dx;
for (unsigned int index=0; index != i2; index++)
val *= dy;
return val;
}
libmesh_error();
return 0.;
#endif
}
RealGradient FE<2,NEDELEC_ONE>::shape(const Elem* elem,
const Order order,
const unsigned int i,
const Point& p)
{
#if LIBMESH_DIM > 1
libmesh_assert(elem);
const Order total_order = static_cast<Order>(order + elem->p_level());
switch (total_order)
{
case FIRST:
{
switch (elem->type())
{
case QUAD8:
case QUAD9:
{
libmesh_assert_less (i, 4);
const Real xi = p(0);
const Real eta = p(1);
// Even with a loose inverse_map tolerance we ought to
// be nearly on the element interior in master
// coordinates
libmesh_assert_less_equal ( std::fabs(xi), 1.0+10*TOLERANCE );
libmesh_assert_less_equal ( std::fabs(eta), 1.0+10*TOLERANCE );
switch(i)
{
case 0:
{
if( elem->point(0) > elem->point(1) )
return RealGradient( -0.25*(1.0-eta), 0.0 );
else
return RealGradient( 0.25*(1.0-eta), 0.0 );
}
case 1:
{
if( elem->point(1) > elem->point(2) )
return RealGradient( 0.0, -0.25*(1.0+xi) );
else
return RealGradient( 0.0, 0.25*(1.0+xi) );
}
case 2:
{
if( elem->point(2) > elem->point(3) )
return RealGradient( 0.25*(1.0+eta), 0.0 );
else
return RealGradient( -0.25*(1.0+eta), 0.0 );
}
case 3:
{
if( elem->point(3) > elem->point(0) )
return RealGradient( 0.0, -0.25*(xi-1.0) );
else
return RealGradient( 0.0, 0.25*(xi-1.0) );
}
default:
libmesh_error();
}
return RealGradient();
}
case TRI6:
{
const Real xi = p(0);
const Real eta = p(1);
libmesh_assert_less (i, 3);
switch(i)
{
case 0:
{
if( elem->point(0) > elem->point(1) )
return RealGradient( -1.0+eta, -xi );
else
return RealGradient( 1.0-eta, xi );
}
case 1:
{
if( elem->point(1) > elem->point(2) )
return RealGradient( eta, -xi );
else
return RealGradient( -eta, xi );
}
case 2:
{
if( elem->point(2) > elem->point(0) )
return RealGradient( eta, -xi+1.0 );
else
return RealGradient( -eta, xi-1.0 );
}
default:
libmesh_error();
}
}
default:
{
libMesh::err << "ERROR: Unsupported 2D element type!: " << elem->type()
<< std::endl;
libmesh_error();
}
}
}
// unsupported order
default:
{
libMesh::err << "ERROR: Unsupported 2D FE order!: " << total_order
<< std::endl;
libmesh_error();
}
}
#endif // LIBMESH_DIM > 1
libmesh_error();
return RealGradient();
}
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;
}
