/*
* \brief This constructor will pull the mesh data DTK needs out of Moab,
* partition it for the example, and build a DataTransferKit::MeshContainer
* object from the local data in the partition. You can directly write the
* traits interface yourself, but this is probably the easiest way to get
* started (although potentially inefficient).
*/
MoabMesh::MoabMesh( const RCP_Comm& comm,
const std::string& filename,
const moab::EntityType& block_topology,
const int partitioning_type )
: d_comm( comm )
{
// Compute the node dimension.
int node_dim = 0;
if ( block_topology == moab::MBTRI )
{
node_dim = 2;
}
else if ( block_topology == moab::MBQUAD )
{
node_dim = 2;
}
else if ( block_topology == moab::MBTET )
{
node_dim = 3;
}
else if ( block_topology == moab::MBHEX )
{
node_dim = 3;
}
else if ( block_topology == moab::MBPYRAMID )
{
node_dim = 3;
}
else
{
node_dim = 0;
}
// Create a moab instance.
moab::ErrorCode error;
d_moab = Teuchos::rcp( new moab::Core() );
std::cout<<"Filename: "<<filename<<std::endl;
// Load the mesh.
d_moab->load_mesh( &filename[0] );
moab::EntityHandle root_set = d_moab->get_root_set();
// Extract the elements with this block's topology.
std::vector<moab::EntityHandle> global_elements;
error = d_moab->get_entities_by_type(
root_set, block_topology, global_elements );
assert( error == moab::MB_SUCCESS );
std::cout<<"Global elements: "<<global_elements.size()<<std::endl;
// Partition the mesh.
int comm_size = d_comm->getSize();
int comm_rank = d_comm->getRank();
// Get the number of nodes in an element.
std::vector<moab::EntityHandle> elem_vertices;
error = d_moab->get_adjacencies( &global_elements[0],
1,
0,
false,
elem_vertices );
assert( error == moab::MB_SUCCESS );
int nodes_per_element = elem_vertices.size();
// Get the global element coordinates.
std::vector<double> global_coords;
error = d_moab->get_vertex_coordinates( global_coords );
assert( error == moab::MB_SUCCESS );
// Get the global max and min values for the coordinates. This problem is
// symmetric.
double min = *(std::min_element( global_coords.begin(),
global_coords.end() ) );
double max = *(std::max_element( global_coords.begin(),
global_coords.end() ) );
double width = max - min;
Teuchos::Array<moab::EntityHandle> elements;
elem_vertices.resize( nodes_per_element );
std::vector<double> elem_coords( 3*nodes_per_element );
std::vector<moab::EntityHandle>::const_iterator global_elem_iterator;
for ( global_elem_iterator = global_elements.begin();
global_elem_iterator != global_elements.end();
++global_elem_iterator )
{
// Get the individual element vertices.
error = d_moab->get_adjacencies( &*global_elem_iterator,
1,
0,
false,
elem_vertices );
assert( error == moab::MB_SUCCESS );
// Get the invidivual element coordinates.
error = d_moab->get_coords( &elem_vertices[0],
elem_vertices.size(),
&elem_coords[0] );
assert( error == moab::MB_SUCCESS );
// Partition in x direction.
if ( partitioning_type == 0 )
{
for ( int i = 0; i < comm_size; ++i )
{
if ( elem_coords[0] >= min + width*(comm_rank)/comm_size - 1e-6 &&
elem_coords[0] <= min + width*(comm_rank+1)/comm_size + 1e-6 )
{
elements.push_back( *global_elem_iterator );
}
}
}
// Partition in y direction.
else if ( partitioning_type == 1 )
{
for ( int i = 0; i < comm_size; ++i )
{
if ( elem_coords[1] >= min + width*(comm_rank)/comm_size - 1e-6 &&
elem_coords[1] <= min + width*(comm_rank+1)/comm_size + 1e-6 )
{
elements.push_back( *global_elem_iterator );
}
}
}
else
{
throw std::logic_error( "Partitioning type not supported." );
}
}
Teuchos::ArrayRCP<moab::EntityHandle> elements_arcp( elements.size() );
std::copy( elements.begin(), elements.end(), elements_arcp.begin() );
elements.clear();
d_comm->barrier();
// Get the nodes.
std::vector<moab::EntityHandle> vertices;
error = d_moab->get_connectivity( &elements_arcp[0],
elements_arcp.size(),
vertices );
assert( error == moab::MB_SUCCESS );
d_vertices = Teuchos::ArrayRCP<moab::EntityHandle>( vertices.size() );
std::copy( vertices.begin(), vertices.end(), d_vertices.begin() );
vertices.clear();
// Get the node coordinates.
Teuchos::ArrayRCP<double> coords( node_dim * d_vertices.size() );
std::vector<double> interleaved_coords( 3*d_vertices.size() );
error = d_moab->get_coords( &d_vertices[0], d_vertices.size(),
&interleaved_coords[0] );
assert( error == moab::MB_SUCCESS );
for ( int n = 0; n < (int) d_vertices.size(); ++n )
{
for ( int d = 0; d < (int) node_dim; ++d )
{
coords[ d*d_vertices.size() + n ] =
interleaved_coords[ n*3 + d ];
}
}
interleaved_coords.clear();
// Get the connectivity.
int connectivity_size = elements_arcp.size() * nodes_per_element;
Teuchos::ArrayRCP<moab::EntityHandle> connectivity( connectivity_size );
std::vector<moab::EntityHandle> elem_conn;
for ( int i = 0; i < (int) elements_arcp.size(); ++i )
{
error = d_moab->get_connectivity( &elements_arcp[i], 1, elem_conn );
assert( error == moab::MB_SUCCESS );
assert( elem_conn.size() ==
Teuchos::as<std::vector<moab::EntityHandle>::size_type>(nodes_per_element) );
for ( int n = 0; n < (int) elem_conn.size(); ++n )
{
connectivity[ n*elements_arcp.size() + i ] = elem_conn[n];
}
}
// Get the permutation vector.
Teuchos::ArrayRCP<int> permutation_list( nodes_per_element );
for ( int i = 0; i < (int) nodes_per_element; ++i )
{
permutation_list[i] = i;
}
// Create the mesh container.
d_mesh_container = Teuchos::rcp(
new Container( node_dim,
d_vertices,
coords,
getTopology(block_topology),
nodes_per_element,
elements_arcp,
connectivity,
permutation_list ) );
}
void YPlus::execute()
{
Mesh& mesh = this->mesh();
// Geometry data
const Field& coords = mesh.geometry_fields().coordinates();
const Uint nb_nodes = coords.size();
const Uint dim = coords.row_size();
// Velocity data
const Field& velocity_field = common::find_component_recursively_with_tag<Field>(mesh, options().value<std::string>("velocity_tag"));
const auto velocity_dict_handle = Handle<Dictionary const>(velocity_field.parent());
cf3_assert(velocity_dict_handle != nullptr);
const Dictionary& velocity_dict = *velocity_dict_handle;
const Uint vel_offset = velocity_field.descriptor().offset("Velocity");
// initialize if needed
auto volume_node_connectivity = Handle<NodeConnectivity>(mesh.get_child("volume_node_connectivity"));
if(m_normals.empty())
{
// Node-to-element connectivity for the volume elements
volume_node_connectivity = mesh.create_component<NodeConnectivity>("volume_node_connectivity");
std::vector< Handle<Entities const> > volume_entities;
for(const mesh::Elements& elements : common::find_components_recursively_with_filter<mesh::Elements>(mesh, IsElementsVolume()))
{
volume_entities.push_back(elements.handle<Entities const>());
}
volume_node_connectivity->initialize(nb_nodes, volume_entities);
mesh.geometry_fields().create_field("wall_velocity_gradient_nodal").add_tag("wall_velocity_gradient_nodal");
Dictionary& wall_P0 = *mesh.create_component<DiscontinuousDictionary>("wall_P0");
m_normals.clear();
for(const Handle<Region>& region : regions())
{
for(mesh::Elements& wall_entity : common::find_components_recursively_with_filter<mesh::Elements>(*region, IsElementsSurface()))
{
const Uint nb_elems = wall_entity.size();
const auto& geom_conn = wall_entity.geometry_space().connectivity();
const ElementType& etype = wall_entity.element_type();
const Uint element_nb_nodes = etype.nb_nodes();
m_normals.push_back(std::vector<RealVector>(nb_elems, RealVector(dim)));
RealMatrix elem_coords(element_nb_nodes, dim);
for(Uint elem_idx = 0; elem_idx != nb_elems; ++elem_idx)
{
const Connectivity::ConstRow conn_row = geom_conn[elem_idx];
fill(elem_coords, coords, conn_row);
RealVector normal(dim);
etype.compute_normal(elem_coords, m_normals.back()[elem_idx]);
m_normals.back()[elem_idx] /= m_normals.back()[elem_idx].norm();
}
wall_entity.create_component<FaceConnectivity>("wall_face_connectivity")->initialize(*volume_node_connectivity);
wall_entity.create_space("cf3.mesh.LagrangeP0."+wall_entity.element_type().shape_name(),wall_P0);
}
}
wall_P0.build(); // to tell the dictionary that all spaces have been added
mesh.update_structures(); // to tell the mesh there is a new dictionary added manually
wall_P0.create_field("wall_velocity_gradient").add_tag("wall_velocity_gradient");
}
// Create the y+ field in the geometry dictionary
if(common::find_component_ptr_with_tag(mesh.geometry_fields(), "yplus") == nullptr)
{
mesh.geometry_fields().create_field("yplus").add_tag("yplus");
}
// Compute shear stress
Uint surface_idx = 0;
Dictionary& wall_P0 = *Handle<mesh::Dictionary>(mesh.get_child_checked("wall_P0"));
Field& wall_velocity_gradient_field = *Handle<Field>(wall_P0.get_child_checked("wall_velocity_gradient"));
for(const Handle<Region>& region : regions())
{
for(const mesh::Elements& elements : common::find_components_recursively_with_filter<mesh::Elements>(*region, IsElementsSurface()))
{
const Uint nb_elements = elements.geometry_space().connectivity().size();
cf3_assert(elements.element_type().nb_faces() == 1);
const auto& face_connectivity = *Handle<FaceConnectivity const>(elements.get_child_checked("wall_face_connectivity"));
const auto& wall_conn = elements.space(wall_P0).connectivity();
for(Uint surface_elm_idx = 0; surface_elm_idx != nb_elements; ++surface_elm_idx)
{
if(face_connectivity.has_adjacent_element(surface_elm_idx, 0))
{
const Uint wall_field_idx = wall_conn[surface_elm_idx][0];
// Get the wall normal vector
const RealVector& normal = m_normals[surface_idx][surface_elm_idx];
RealVector3 normal3;
normal3[0] = normal[0];
normal3[1] = normal[1];
normal3[2] = dim == 3 ? normal[2] : 0.;
// The connected volume element
NodeConnectivity::ElementReferenceT connected = face_connectivity.adjacent_element(surface_elm_idx, 0);
const mesh::Entities& volume_entities = *face_connectivity.node_connectivity().entities()[connected.first];
const Uint volume_elem_idx = connected.second;
const auto& velocity_conn = volume_entities.space(velocity_dict).connectivity();
const auto& velocity_sf = volume_entities.space(velocity_dict).shape_function();
const auto& geom_conn = volume_entities.geometry_space().connectivity();
const ElementType& volume_etype = volume_entities.element_type();
const Uint nb_vel_nodes = velocity_sf.nb_nodes();
const RealVector centroid_mapped_coord = 0.5*(velocity_sf.local_coordinates().colwise().minCoeff() + velocity_sf.local_coordinates().colwise().maxCoeff());
RealMatrix elem_coords(geom_conn.row_size(), dim);
fill(elem_coords, coords, geom_conn[volume_elem_idx]);
RealVector tangential_velocity(nb_vel_nodes); // For every node, the component of the velocity tangential to the wall
RealVector3 v3;
for(Uint i = 0; i != nb_vel_nodes; ++i)
{
Eigen::Map<RealVector const> v(&velocity_field[velocity_conn[volume_elem_idx][i]][vel_offset], dim);
v3[0] = v[0];
v3[1] = v[1];
v3[2] = dim == 3 ? v[2] : 0.;
tangential_velocity[i] = v3.cross(normal3).norm();
}
wall_velocity_gradient_field[wall_field_idx][0] = fabs((volume_etype.jacobian(centroid_mapped_coord, elem_coords).inverse() * velocity_sf.gradient(centroid_mapped_coord) * tangential_velocity).dot(-normal));
}
}
++surface_idx;
}
}
wall_velocity_gradient_field.synchronize();
// Compute a nodal version of the wall velocity gradient
const auto& wall_node_connectivity = *Handle<NodeConnectivity>(mesh.get_child_checked("wall_node_connectivity"));
Field& wall_velocity_gradient_field_nodal = *Handle<Field>(mesh.geometry_fields().get_child_checked("wall_velocity_gradient_nodal"));
for(Uint node_idx = 0; node_idx != nb_nodes; ++node_idx)
{
Uint nb_connected_elems = 0;
wall_velocity_gradient_field_nodal[node_idx][0] = 0;
for(const NodeConnectivity::ElementReferenceT elref : wall_node_connectivity.node_element_range(node_idx))
{
const Uint wall_field_idx = wall_node_connectivity.entities()[elref.first]->space(wall_P0).connectivity()[elref.second][0];
wall_velocity_gradient_field_nodal[node_idx][0] += wall_velocity_gradient_field[wall_field_idx][0];
++nb_connected_elems;
}
if(nb_connected_elems != 0)
{
wall_velocity_gradient_field_nodal[node_idx][0] /= static_cast<Real>(nb_connected_elems);
}
}
// Set Yplus
Field& yplus_field = *Handle<Field>(mesh.geometry_fields().get_child_checked("yplus"));
const Field& wall_distance_field = *Handle<Field>(mesh.geometry_fields().get_child_checked("wall_distance"));
const auto& node_to_wall_element = *Handle<common::Table<Uint>>(mesh.get_child_checked("node_to_wall_element"));
const Real nu = physical_model().options().value<Real>("kinematic_viscosity");
for(Uint node_idx = 0; node_idx != nb_nodes; ++node_idx)
{
yplus_field[node_idx][0] = 0;
if(node_to_wall_element[node_idx][0] != 0)
{
const Entities& wall_entities = *wall_node_connectivity.entities()[node_to_wall_element[node_idx][1]];
const Uint wall_field_idx = wall_entities.space(wall_P0).connectivity()[node_to_wall_element[node_idx][2]][0];
yplus_field[node_idx][0] = wall_distance_field[node_idx][0] * sqrt(nu*wall_velocity_gradient_field[wall_field_idx][0]) / nu;
}
else
{
yplus_field[node_idx][0] = wall_distance_field[node_idx][0] * sqrt(nu*wall_velocity_gradient_field_nodal[node_to_wall_element[node_idx][1]][0]) / nu;
}
}
}
