Ioss::IntVector Ioss::TriShell6::edge_connectivity(int edge_number) const
{
assert(edge_number > 0 && edge_number <= Constants::nedge);
Ioss::IntVector connectivity(Constants::nedgenode);
for (int i = 0; i < Constants::nedgenode; i++) {
connectivity[i] = Constants::edge_node_order[edge_number - 1][i];
}
return connectivity;
}
Ioss::IntVector Ioss::Wedge16::face_connectivity(int face_number) const
{
assert(face_number > 0 && face_number <= number_faces());
Ioss::IntVector connectivity(number_nodes_face(face_number));
for (int i = 0; i < number_nodes_face(face_number); i++) {
connectivity[i] = Constants::face_node_order[face_number - 1][i];
}
return connectivity;
}
Ioss::IntVector Ioss::TriShell6::face_connectivity(int face_number) const
{
assert(face_number > 0 && face_number <= number_faces());
Ioss::IntVector connectivity(Constants::nodes_per_face[face_number]);
for (int i = 0; i < Constants::nodes_per_face[face_number]; i++) {
connectivity[i] = Constants::face_node_order[face_number - 1][i];
}
return connectivity;
}
TEUCHOS_UNIT_TEST(tOrientation, testFaceBasis_tet)
{
out << note << std::endl;
// basis to build patterns from
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisA = rcp(new Intrepid2::Basis_HGRAD_TET_C1_FEM<PHX::exec_space,double,double>);
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisB = rcp(new Intrepid2::Basis_HDIV_TET_I1_FEM<PHX::exec_space,double,double>);
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisC = rcp(new Intrepid2::Basis_HGRAD_TET_C2_FEM<PHX::exec_space,double,double>); // used further down
RCP<const FieldPattern> patternA = rcp(new Intrepid2FieldPattern(basisA));
RCP<const FieldPattern> patternB = rcp(new Intrepid2FieldPattern(basisB));
RCP<const FieldPattern> patternC = rcp(new Intrepid2FieldPattern(basisC)); // used further down
TEST_EQUALITY(patternA->numberIds(),4);
TEST_EQUALITY(patternB->numberIds(),4);
std::vector<std::vector<int> > topFaceIndices;
orientation_helpers::computePatternFaceIndices(*patternA,topFaceIndices);
TEST_EQUALITY(topFaceIndices.size(),4);
TEST_EQUALITY(topFaceIndices[0].size(),3); TEST_EQUALITY(topFaceIndices[0][0],0); TEST_EQUALITY(topFaceIndices[0][1],1); TEST_EQUALITY(topFaceIndices[0][2],3);
TEST_EQUALITY(topFaceIndices[1].size(),3); TEST_EQUALITY(topFaceIndices[1][0],1); TEST_EQUALITY(topFaceIndices[1][1],2); TEST_EQUALITY(topFaceIndices[1][2],3);
TEST_EQUALITY(topFaceIndices[2].size(),3); TEST_EQUALITY(topFaceIndices[2][0],0); TEST_EQUALITY(topFaceIndices[2][1],3); TEST_EQUALITY(topFaceIndices[2][2],2);
TEST_EQUALITY(topFaceIndices[3].size(),3); TEST_EQUALITY(topFaceIndices[3][0],0); TEST_EQUALITY(topFaceIndices[3][1],2); TEST_EQUALITY(topFaceIndices[3][2],1);
// Topologically the first elements look like (shown by looking at each face), note
// that the expected orientation is included as a +/- sign in the element
// //
// 7 7 7 2 //
// / \ / \ / \ / \ //
// / - \ / - \ / + \ / + \ //
// / \ / \ / \ / \ //
// 6 ----- 2 2 ----- 9 9 ----- 6 6 ----- 9 //
// //
// all that matters is the global
// node numbering and the local ordering
// The local ordering is defined by the following connectivity
std::vector<std::vector<long> > connectivity(1);
connectivity[0].resize(patternA->numberIds());
connectivity[0][0] = 6; connectivity[0][1] = 2; connectivity[0][2] = 9; connectivity[0][3] = 7;
{
std::vector<char> orientations(patternB->numberIds(),0);
orientation_helpers::computeCellFaceOrientations(topFaceIndices, connectivity[0], *patternB, orientations);
TEST_EQUALITY(orientations[0],char(-1));
TEST_EQUALITY(orientations[1],char(-1));
TEST_EQUALITY(orientations[2],char(1));
TEST_EQUALITY(orientations[3],char(1));
}
}
Ioss::IntVector Ioss::ShellLine2D3::edge_connectivity(int edge_number) const
{
Ioss::IntVector connectivity(Constants::nedgenode);
if (edge_number == 1) {
connectivity[0] = 0;
connectivity[1] = 1;
connectivity[2] = 2;
} else {
connectivity[0] = 1;
connectivity[1] = 0;
connectivity[2] = 2;
}
return connectivity;
}
//--------------------------------------------------------------------------
void
PromotedElementIO::write_element_connectivity(
const stk::mesh::PartVector& baseParts,
const std::vector<stk::mesh::EntityId>& entityIds)
{
for(const auto* ip : baseParts) {
const stk::mesh::Part& part = *ip;
if(part.topology().rank() !=stk::topology::ELEM_RANK) {
continue;
}
const auto& selector = metaData_.locally_owned_part() & part;
const auto& elemBuckets = bulkData_.get_buckets(stk::topology::ELEM_RANK, selector);
const size_t numSubElementsInBlock = num_sub_elements(nDim_, elemBuckets, elem_.polyOrder);
const unsigned nodesPerLinearElem = elem_.nodesPerSubElement;
std::vector<int64_t> connectivity(nodesPerLinearElem*numSubElementsInBlock);
std::vector<int64_t> globalSubElementIds(numSubElementsInBlock);
int connIndex = 0;
unsigned subElementCounter = 0;
for (const auto* ib: elemBuckets) {
const stk::mesh::Bucket& b = *ib;
const auto length = b.size();
for (size_t k = 0; k < length; ++k) {
const auto* node_rels = b.begin_nodes(k);
const auto& subElems = elem_.subElementConnectivity;
const auto numberSubElements = subElems.size();
for (unsigned subElementIndex = 0; subElementIndex < numberSubElements; ++subElementIndex) {
globalSubElementIds.at(subElementCounter) = entityIds[subElementCounter];
const auto& localIndices = subElems.at(subElementIndex);
for (unsigned j = 0; j < nodesPerLinearElem; ++j) {
connectivity[connIndex] = bulkData_.identifier(node_rels[localIndices[j]]);
++connIndex;
}
++subElementCounter;
}
}
}
elementBlockPointers_.at(ip)->put_field_data("ids", globalSubElementIds);
elementBlockPointers_.at(ip)->put_field_data("connectivity", connectivity);
}
}
void mesh_basic::fill_normal()
{
int const N_vertex=size_vertex();
if(size_normal()!=N_vertex)
normal_data.resize(N_vertex);
//init normal data to 0
for(auto& n : normal_data)
n=vec3();
//walk through all the triangles and add each triangle normal to the vertices
int const N_triangle=size_connectivity();
for(int k_triangle=0;k_triangle<N_triangle;++k_triangle)
{
//get current triangle index
triangle_index const& tri=connectivity(k_triangle);
//check that the index given have correct values
ASSERT_CPE(tri.u0()>=0 && tri.u0()<N_vertex,"Incorrect triangle index");
ASSERT_CPE(tri.u1()>=0 && tri.u1()<N_vertex,"Incorrect triangle index");
ASSERT_CPE(tri.u2()>=0 && tri.u2()<N_vertex,"Incorrect triangle index");
//compute current normal
vec3 const& p0=vertex(tri.u0());
vec3 const& p1=vertex(tri.u1());
vec3 const& p2=vertex(tri.u2());
vec3 const u1=normalized(p1-p0);
vec3 const u2=normalized(p2-p0);
vec3 const n=normalized(cross(u1,u2));
//add the computed normal to the normal_data
for(int kv=0;kv<3;++kv)
normal_data[tri[kv]] += n;
}
//normalize all normal value
for(auto& n : normal_data)
n=normalized(n);
}
void MeshUtility::calculateNormals(Vector3* vertices, UINT8* indices, UINT32 numVertices,
UINT32 numIndices, Vector3* normals, UINT32 indexSize)
{
UINT32 numFaces = numIndices / 3;
Vector3* faceNormals = bs_newN<Vector3>(numFaces);
for (UINT32 i = 0; i < numFaces; i++)
{
UINT32 triangle[3];
memcpy(&triangle[0], indices + (i * 3 + 0) * indexSize, indexSize);
memcpy(&triangle[1], indices + (i * 3 + 1) * indexSize, indexSize);
memcpy(&triangle[2], indices + (i * 3 + 2) * indexSize, indexSize);
Vector3 edgeA = vertices[triangle[1]] - vertices[triangle[0]];
Vector3 edgeB = vertices[triangle[2]] - vertices[triangle[0]];
faceNormals[i] = Vector3::normalize(Vector3::cross(edgeA, edgeB));
// Note: Potentially don't normalize here in order to weigh the normals
// by triangle size
}
VertexConnectivity connectivity(indices, numVertices, numFaces, indexSize);
for (UINT32 i = 0; i < numVertices; i++)
{
VertexFaces& faces = connectivity.vertexFaces[i];
normals[i] = Vector3::ZERO;
for (UINT32 j = 0; j < faces.numFaces; j++)
{
UINT32 faceIdx = faces.faces[j];
normals[i] += faceNormals[faceIdx];
}
normals[i].normalize();
}
bs_deleteN(faceNormals, numFaces);
}
void MeshUtility::calculateTangents(Vector3* vertices, Vector3* normals, Vector2* uv, UINT8* indices, UINT32 numVertices,
UINT32 numIndices, Vector3* tangents, Vector3* bitangents, UINT32 indexSize, UINT32 vertexStride)
{
UINT32 numFaces = numIndices / 3;
UINT32 vec2Stride = vertexStride == 0 ? sizeof(Vector2) : vertexStride;
UINT32 vec3Stride = vertexStride == 0 ? sizeof(Vector3) : vertexStride;
UINT8* positionBytes = (UINT8*)vertices;
UINT8* normalBytes = (UINT8*)normals;
UINT8* uvBytes = (UINT8*)uv;
Vector3* faceTangents = bs_newN<Vector3>(numFaces);
Vector3* faceBitangents = bs_newN<Vector3>(numFaces);
for (UINT32 i = 0; i < numFaces; i++)
{
UINT32 triangle[3];
memcpy(&triangle[0], indices + (i * 3 + 0) * indexSize, indexSize);
memcpy(&triangle[1], indices + (i * 3 + 1) * indexSize, indexSize);
memcpy(&triangle[2], indices + (i * 3 + 2) * indexSize, indexSize);
Vector3 p0 = *(Vector3*)&positionBytes[triangle[0] * vec3Stride];
Vector3 p1 = *(Vector3*)&positionBytes[triangle[1] * vec3Stride];
Vector3 p2 = *(Vector3*)&positionBytes[triangle[2] * vec3Stride];
Vector2 uv0 = *(Vector2*)&uvBytes[triangle[0] * vec2Stride];
Vector2 uv1 = *(Vector2*)&uvBytes[triangle[1] * vec2Stride];
Vector2 uv2 = *(Vector2*)&uvBytes[triangle[2] * vec2Stride];
Vector3 q0 = p1 - p0;
Vector3 q1 = p2 - p0;
Vector2 st1 = uv1 - uv0;
Vector2 st2 = uv2 - uv0;
float denom = st1.x * st2.y - st2.x * st1.y;
if (fabs(denom) >= 0e-8f)
{
float r = 1.0f / denom;
faceTangents[i] = (st2.y * q0 - st1.y * q1) * r;
faceBitangents[i] = (st1.x * q1 - st2.x * q0) * r;
faceTangents[i].normalize();
faceBitangents[i].normalize();
}
// Note: Potentially don't normalize here in order to weight the normals by triangle size
}
VertexConnectivity connectivity(indices, numVertices, numFaces, indexSize);
for (UINT32 i = 0; i < numVertices; i++)
{
VertexFaces& faces = connectivity.vertexFaces[i];
tangents[i] = Vector3::ZERO;
bitangents[i] = Vector3::ZERO;
for (UINT32 j = 0; j < faces.numFaces; j++)
{
UINT32 faceIdx = faces.faces[j];
tangents[i] += faceTangents[faceIdx];
bitangents[i] += faceBitangents[faceIdx];
}
tangents[i].normalize();
bitangents[i].normalize();
Vector3 normal = *(Vector3*)&normalBytes[i * vec3Stride];
// Orthonormalize
float dot0 = normal.dot(tangents[i]);
tangents[i] -= dot0*normal;
tangents[i].normalize();
float dot1 = tangents[i].dot(bitangents[i]);
dot0 = normal.dot(bitangents[i]);
bitangents[i] -= dot0*normal + dot1*tangents[i];
bitangents[i].normalize();
}
bs_deleteN(faceTangents, numFaces);
bs_deleteN(faceBitangents, numFaces);
// TODO - Consider weighing tangents by triangle size and/or edge angles
}
DTKAdapter::DTKAdapter(Teuchos::RCP<const Teuchos::Comm<int> > in_comm, EquationSystems & in_es):
comm(in_comm),
es(in_es),
mesh(in_es.get_mesh()),
dim(mesh.mesh_dimension())
{
std::set<unsigned int> semi_local_nodes;
get_semi_local_nodes(semi_local_nodes);
num_local_nodes = semi_local_nodes.size();
vertices.resize(num_local_nodes);
Teuchos::ArrayRCP<double> coordinates(num_local_nodes * dim);
// Fill in the vertices and coordinates
{
unsigned int i = 0;
for(std::set<unsigned int>::iterator it = semi_local_nodes.begin();
it != semi_local_nodes.end();
++it)
{
const Node & node = mesh.node(*it);
vertices[i] = node.id();
for(unsigned int j=0; j<dim; j++)
coordinates[(j*num_local_nodes) + i] = node(j);
i++;
}
}
// Currently assuming all elements are the same!
DataTransferKit::DTK_ElementTopology element_topology = get_element_topology(mesh.elem(0));
unsigned int n_nodes_per_elem = mesh.elem(0)->n_nodes();
unsigned int n_local_elem = mesh.n_local_elem();
Teuchos::ArrayRCP<int> elements(n_local_elem);
Teuchos::ArrayRCP<int> connectivity(n_nodes_per_elem*n_local_elem);
// Fill in the elements and connectivity
{
unsigned int i = 0;
MeshBase::const_element_iterator end = mesh.local_elements_end();
for(MeshBase::const_element_iterator it = mesh.local_elements_begin();
it != end;
++it)
{
const Elem & elem = *(*it);
elements[i] = elem.id();
for(unsigned int j=0; j<n_nodes_per_elem; j++)
connectivity[(j*n_local_elem)+i] = elem.node(j);
i++;
}
}
Teuchos::ArrayRCP<int> permutation_list(n_nodes_per_elem);
for (unsigned int i = 0; i < n_nodes_per_elem; ++i )
permutation_list[i] = i;
/*
if(this->processor_id() == 1)
sleep(1);
libMesh::out<<"n_nodes_per_elem: "<<n_nodes_per_elem<<std::endl;
libMesh::out<<"Dim: "<<dim<<std::endl;
libMesh::err<<"Vertices size: "<<vertices.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Vertices: ";
for(unsigned int i=0; i<vertices.size(); i++)
libMesh::err<<vertices[i]<<" ";
libMesh::err<<std::endl;
}
libMesh::err<<"Coordinates size: "<<coordinates.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Coordinates: ";
for(unsigned int i=0; i<coordinates.size(); i++)
libMesh::err<<coordinates[i]<<" ";
libMesh::err<<std::endl;
}
libMesh::err<<"Connectivity size: "<<connectivity.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Connectivity: ";
for(unsigned int i=0; i<connectivity.size(); i++)
libMesh::err<<connectivity[i]<<" ";
libMesh::err<<std::endl;
}
libMesh::err<<"Permutation_List size: "<<permutation_list.size()<<std::endl;
{
libMesh::err<<this->processor_id()<<" Permutation_List: ";
for(unsigned int i=0; i<permutation_list.size(); i++)
libMesh::err<<permutation_list[i]<<" ";
libMesh::err<<std::endl;
}
*/
Teuchos::RCP<MeshContainerType> mesh_container = Teuchos::rcp(
new MeshContainerType(dim, vertices, coordinates,
element_topology, n_nodes_per_elem,
elements, connectivity, permutation_list) );
// We only have 1 element topology in this grid so we make just one mesh block
Teuchos::ArrayRCP<Teuchos::RCP<MeshContainerType> > mesh_blocks(1);
mesh_blocks[0] = mesh_container;
// Create the MeshManager
mesh_manager = Teuchos::rcp(new DataTransferKit::MeshManager<MeshContainerType>(mesh_blocks, comm, dim) );
// Pack the coordinates into a field, this will be the positions we'll ask for other systems fields at
target_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(mesh_container, comm));
}
// Block now checks to see if nodes i and j are connected and, if
// so, uses our alternative spring function.
loos::DoubleMatrix block(const uint j, const uint i) {
if (connectivity(j, i))
return(blockImpl(j, i, bound_spring));
else
return(decorated->block(j, i));
}
Ioss::IntVector Ioss::Edge2::edge_connectivity(int /* edge_number */) const
{
Ioss::IntVector connectivity(Constants::nedgenode);
return connectivity;
}
void grpc_end2end_tests(int argc, char **argv,
grpc_end2end_test_config config) {
int i;
GPR_ASSERT(g_pre_init_called);
if (argc <= 1) {
authority_not_supported(config);
bad_hostname(config);
binary_metadata(config);
call_creds(config);
cancel_after_accept(config);
cancel_after_client_done(config);
cancel_after_invoke(config);
cancel_before_invoke(config);
cancel_in_a_vacuum(config);
cancel_with_status(config);
compressed_payload(config);
connectivity(config);
default_host(config);
disappearing_server(config);
empty_batch(config);
filter_call_init_fails(config);
filter_causes_close(config);
filter_latency(config);
graceful_server_shutdown(config);
high_initial_seqno(config);
hpack_size(config);
idempotent_request(config);
invoke_large_request(config);
large_metadata(config);
load_reporting_hook(config);
max_concurrent_streams(config);
max_message_length(config);
negative_deadline(config);
network_status_change(config);
no_logging(config);
no_op(config);
payload(config);
ping(config);
ping_pong_streaming(config);
registered_call(config);
request_with_flags(config);
request_with_payload(config);
resource_quota_server(config);
server_finishes_request(config);
shutdown_finishes_calls(config);
shutdown_finishes_tags(config);
simple_cacheable_request(config);
simple_delayed_request(config);
simple_metadata(config);
simple_request(config);
streaming_error_response(config);
trailing_metadata(config);
return;
}
for (i = 1; i < argc; i++) {
if (0 == strcmp("authority_not_supported", argv[i])) {
authority_not_supported(config);
continue;
}
if (0 == strcmp("bad_hostname", argv[i])) {
bad_hostname(config);
continue;
}
if (0 == strcmp("binary_metadata", argv[i])) {
binary_metadata(config);
continue;
}
if (0 == strcmp("call_creds", argv[i])) {
call_creds(config);
continue;
}
if (0 == strcmp("cancel_after_accept", argv[i])) {
cancel_after_accept(config);
continue;
}
if (0 == strcmp("cancel_after_client_done", argv[i])) {
cancel_after_client_done(config);
continue;
}
if (0 == strcmp("cancel_after_invoke", argv[i])) {
cancel_after_invoke(config);
continue;
}
if (0 == strcmp("cancel_before_invoke", argv[i])) {
cancel_before_invoke(config);
continue;
}
if (0 == strcmp("cancel_in_a_vacuum", argv[i])) {
cancel_in_a_vacuum(config);
continue;
}
if (0 == strcmp("cancel_with_status", argv[i])) {
cancel_with_status(config);
continue;
}
if (0 == strcmp("compressed_payload", argv[i])) {
compressed_payload(config);
continue;
}
if (0 == strcmp("connectivity", argv[i])) {
connectivity(config);
continue;
}
if (0 == strcmp("default_host", argv[i])) {
default_host(config);
continue;
}
if (0 == strcmp("disappearing_server", argv[i])) {
disappearing_server(config);
continue;
}
if (0 == strcmp("empty_batch", argv[i])) {
empty_batch(config);
continue;
}
if (0 == strcmp("filter_call_init_fails", argv[i])) {
filter_call_init_fails(config);
continue;
}
if (0 == strcmp("filter_causes_close", argv[i])) {
filter_causes_close(config);
continue;
}
if (0 == strcmp("filter_latency", argv[i])) {
filter_latency(config);
continue;
}
if (0 == strcmp("graceful_server_shutdown", argv[i])) {
graceful_server_shutdown(config);
continue;
}
if (0 == strcmp("high_initial_seqno", argv[i])) {
high_initial_seqno(config);
continue;
}
if (0 == strcmp("hpack_size", argv[i])) {
hpack_size(config);
continue;
}
if (0 == strcmp("idempotent_request", argv[i])) {
idempotent_request(config);
continue;
}
if (0 == strcmp("invoke_large_request", argv[i])) {
invoke_large_request(config);
continue;
}
if (0 == strcmp("large_metadata", argv[i])) {
large_metadata(config);
continue;
}
if (0 == strcmp("load_reporting_hook", argv[i])) {
load_reporting_hook(config);
continue;
}
if (0 == strcmp("max_concurrent_streams", argv[i])) {
max_concurrent_streams(config);
continue;
}
if (0 == strcmp("max_message_length", argv[i])) {
max_message_length(config);
continue;
}
if (0 == strcmp("negative_deadline", argv[i])) {
negative_deadline(config);
continue;
}
if (0 == strcmp("network_status_change", argv[i])) {
network_status_change(config);
continue;
}
if (0 == strcmp("no_logging", argv[i])) {
no_logging(config);
continue;
}
if (0 == strcmp("no_op", argv[i])) {
no_op(config);
continue;
}
if (0 == strcmp("payload", argv[i])) {
payload(config);
continue;
}
if (0 == strcmp("ping", argv[i])) {
ping(config);
continue;
}
if (0 == strcmp("ping_pong_streaming", argv[i])) {
ping_pong_streaming(config);
continue;
}
if (0 == strcmp("registered_call", argv[i])) {
registered_call(config);
continue;
}
if (0 == strcmp("request_with_flags", argv[i])) {
request_with_flags(config);
continue;
}
if (0 == strcmp("request_with_payload", argv[i])) {
request_with_payload(config);
continue;
}
if (0 == strcmp("resource_quota_server", argv[i])) {
resource_quota_server(config);
continue;
}
if (0 == strcmp("server_finishes_request", argv[i])) {
server_finishes_request(config);
continue;
}
if (0 == strcmp("shutdown_finishes_calls", argv[i])) {
shutdown_finishes_calls(config);
continue;
}
if (0 == strcmp("shutdown_finishes_tags", argv[i])) {
shutdown_finishes_tags(config);
continue;
}
if (0 == strcmp("simple_cacheable_request", argv[i])) {
simple_cacheable_request(config);
continue;
}
if (0 == strcmp("simple_delayed_request", argv[i])) {
simple_delayed_request(config);
continue;
}
if (0 == strcmp("simple_metadata", argv[i])) {
simple_metadata(config);
continue;
}
if (0 == strcmp("simple_request", argv[i])) {
simple_request(config);
continue;
}
if (0 == strcmp("streaming_error_response", argv[i])) {
streaming_error_response(config);
continue;
}
if (0 == strcmp("trailing_metadata", argv[i])) {
trailing_metadata(config);
continue;
}
gpr_log(GPR_DEBUG, "not a test: '%s'", argv[i]);
abort();
}
}
/*!
* \brief Get the wave mesh.
*/
Teuchos::RCP<DataTransferKit::MeshManager<WaveAdapter::MeshType> >
WaveAdapter::getMesh( const RCP_Wave& wave )
{
// Get the process rank.
int my_rank = wave->get_comm()->getRank();
// Set the vertex dimension - this is a 1D problem.
int vertex_dimension = 1;
// Compute globally unique vertex ids.
Teuchos::RCP<std::vector<double> > grid = wave->get_grid();
Teuchos::ArrayRCP<int> vertices( grid->size() );
for ( int i = 0; i < (int) vertices.size(); ++i )
{
vertices[i] = i + my_rank*vertices.size();
}
// Get the grid vertex coordinates.
Teuchos::ArrayRCP<double> coordinates( &(*grid)[0], 0, grid->size(), false );
// Set the grid topology - this is 1D so we are using line segments.
DataTransferKit::DTK_ElementTopology element_topology =
DataTransferKit::DTK_LINE_SEGMENT;
// Each line segment will be constructed by 2 vertices.
int vertices_per_element = 2;
// Compute globally unique element ids.
Teuchos::ArrayRCP<int> elements( grid->size() - 1 );
for ( int i = 0; i < (int) elements.size(); ++i )
{
elements[i] = i + my_rank*elements.size();
}
// Generate element connectivity. The global vertex ids are used to
// describe the construction of each line segment.
Teuchos::ArrayRCP<int> connectivity( vertices_per_element*elements.size() );
for ( int i = 0; i < (int) elements.size(); ++i )
{
connectivity[i] = vertices[i];
connectivity[ elements.size() + i ] = vertices[i+1];
}
// Define the permutation list. Here our line segments are ordered the
// same as DTK canonical ordering so the list is an monotonically
// increasing set of integers.
Teuchos::ArrayRCP<int> permutation_list( vertices_per_element );
for ( int i = 0; i < vertices_per_element; ++i )
{
permutation_list[i] = i;
}
// Build a DTK Mesh container with the data. The MeshType typedef is set
// in the header file.
Teuchos::RCP<MeshType> mesh_container = Teuchos::rcp(
new MeshType( vertex_dimension, vertices, coordinates,
element_topology, vertices_per_element,
elements, connectivity, permutation_list ) );
// We only have 1 element topology in this grid so we make just one mesh
// block.
Teuchos::ArrayRCP<Teuchos::RCP<MeshType> > mesh_blocks( 1 );
mesh_blocks[0] = mesh_container;
// Return a mesh manager.
return Teuchos::rcp( new DataTransferKit::MeshManager<MeshType>(
mesh_blocks, wave->get_comm(), 1 ) );
}
Ioss::IntVector Ioss::Super::edge_connectivity(int edge_number) const
{
Ioss::IntVector connectivity(0);
return connectivity;
}
/*
* \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 ) );
}
TEUCHOS_UNIT_TEST(tOrientation, testFaceBasis_hex)
{
out << note << std::endl;
// basis to build patterns from
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisA = rcp(new Intrepid2::Basis_HGRAD_HEX_C1_FEM<PHX::exec_space,double,double>);
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisB = rcp(new Intrepid2::Basis_HDIV_HEX_I1_FEM<PHX::exec_space,double,double>);
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisC = rcp(new Intrepid2::Basis_HGRAD_HEX_C2_FEM<PHX::exec_space,double,double>); // used further down
RCP<const FieldPattern> patternA = rcp(new Intrepid2FieldPattern(basisA));
RCP<const FieldPattern> patternB = rcp(new Intrepid2FieldPattern(basisB));
RCP<const FieldPattern> patternC = rcp(new Intrepid2FieldPattern(basisC)); // used further down
TEST_EQUALITY(patternA->numberIds(),8);
TEST_EQUALITY(patternB->numberIds(),6);
std::vector<std::vector<int> > topFaceIndices;
orientation_helpers::computePatternFaceIndices(*patternA,topFaceIndices);
// this checks to ensure that each face is oriented in a counter clockwise direction
TEST_EQUALITY(topFaceIndices.size(),6);
TEST_EQUALITY(topFaceIndices[0].size(),4);
TEST_EQUALITY(topFaceIndices[0][0],0); TEST_EQUALITY(topFaceIndices[0][1],1); TEST_EQUALITY(topFaceIndices[0][2],5); TEST_EQUALITY(topFaceIndices[0][3],4);
TEST_EQUALITY(topFaceIndices[1].size(),4);
TEST_EQUALITY(topFaceIndices[1][0],1); TEST_EQUALITY(topFaceIndices[1][1],2); TEST_EQUALITY(topFaceIndices[1][2],6); TEST_EQUALITY(topFaceIndices[1][3],5);
TEST_EQUALITY(topFaceIndices[2].size(),4);
TEST_EQUALITY(topFaceIndices[2][0],2); TEST_EQUALITY(topFaceIndices[2][1],3); TEST_EQUALITY(topFaceIndices[2][2],7); TEST_EQUALITY(topFaceIndices[2][3],6);
TEST_EQUALITY(topFaceIndices[3].size(),4);
TEST_EQUALITY(topFaceIndices[3][0],0); TEST_EQUALITY(topFaceIndices[3][1],4); TEST_EQUALITY(topFaceIndices[3][2],7); TEST_EQUALITY(topFaceIndices[3][3],3);
TEST_EQUALITY(topFaceIndices[4].size(),4);
TEST_EQUALITY(topFaceIndices[4][0],0); TEST_EQUALITY(topFaceIndices[4][1],3); TEST_EQUALITY(topFaceIndices[4][2],2); TEST_EQUALITY(topFaceIndices[4][3],1);
TEST_EQUALITY(topFaceIndices[5].size(),4);
TEST_EQUALITY(topFaceIndices[5][0],4); TEST_EQUALITY(topFaceIndices[5][1],5); TEST_EQUALITY(topFaceIndices[5][2],6); TEST_EQUALITY(topFaceIndices[5][3],7);
// Topologically the first elements look like (shown by looking at each face), note
// that the expected orientation is included as a +/- sign in the element
//
// 0 ----- 8 8 ----- 9 9 ----- 1
// | | | | | |
// | + | | + | | - |
// | | | | | |
// 5 ----- 2 2 ----- 6 6 ----- 7
//
// 1 ----- 0 5 ----- 2 1 ----- 9
// | | | | | |
// | + | | + | | - |
// | | | | | |
// 7 ----- 5 7 ----- 6 0 ----- 8
//
// all that matters is the global
// node numbering and the local ordering
// The local ordering is defined by the following connectivity
std::vector<std::vector<long> > connectivity(1);
connectivity[0].resize(patternA->numberIds());
connectivity[0][0] = 5; connectivity[0][1] = 2; connectivity[0][2] = 6; connectivity[0][3] = 7;
connectivity[0][4] = 0; connectivity[0][5] = 8; connectivity[0][6] = 9; connectivity[0][7] = 1;
{
std::vector<char> orientations(patternB->numberIds(),0);
orientation_helpers::computeCellFaceOrientations(topFaceIndices, connectivity[0], *patternB, orientations);
TEST_EQUALITY(orientations[0],char(1));
TEST_EQUALITY(orientations[1],char(1));
TEST_EQUALITY(orientations[2],char(-1));
TEST_EQUALITY(orientations[3],char(1));
TEST_EQUALITY(orientations[4],char(1));
TEST_EQUALITY(orientations[5],char(-1));
}
}
TEUCHOS_UNIT_TEST(tOrientation, testEdgeBasis_tri)
{
out << note << std::endl;
// basis to build patterns from
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisA = rcp(new Intrepid2::Basis_HGRAD_TRI_C1_FEM<PHX::exec_space,double,double>);
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisB = rcp(new Intrepid2::Basis_HCURL_TRI_I1_FEM<PHX::exec_space,double,double>);
RCP<Intrepid2::Basis<PHX::exec_space,double,double> > basisC = rcp(new Intrepid2::Basis_HGRAD_TRI_C2_FEM<PHX::exec_space,double,double>); // used further down
RCP<const FieldPattern> patternA = rcp(new Intrepid2FieldPattern(basisA));
RCP<const FieldPattern> patternB = rcp(new Intrepid2FieldPattern(basisB));
RCP<const FieldPattern> patternC = rcp(new Intrepid2FieldPattern(basisC)); // used further down
TEST_EQUALITY(patternA->numberIds(),3);
TEST_EQUALITY(patternB->numberIds(),3);
std::vector<std::pair<int,int> > topEdgeIndices;
orientation_helpers::computePatternEdgeIndices(*patternA,topEdgeIndices);
TEST_EQUALITY(topEdgeIndices.size(),3);
TEST_EQUALITY(topEdgeIndices[0].first,0); TEST_EQUALITY(topEdgeIndices[0].second,1);
TEST_EQUALITY(topEdgeIndices[1].first,1); TEST_EQUALITY(topEdgeIndices[1].second,2);
TEST_EQUALITY(topEdgeIndices[2].first,2); TEST_EQUALITY(topEdgeIndices[2].second,0);
std::vector<std::vector<long> > connectivity(4);
connectivity[0].resize(patternA->numberIds());
connectivity[1].resize(patternA->numberIds());
connectivity[2].resize(patternA->numberIds());
connectivity[3].resize(patternA->numberIds());
// Topologocally the four elements look like:
//
// 3-----1
// |\ /|
// | \ / |
// | 6 |
// | / \ |
// |/ \|
// 5-----0
//
// all that matters is the global
// node numbering and the local ordering
// The local ordering is defined by the following connectivity
connectivity[0][0] = 0; connectivity[0][1] = 6; connectivity[0][2] = 5;
connectivity[1][0] = 6; connectivity[1][1] = 0; connectivity[1][2] = 1;
connectivity[2][0] = 1; connectivity[2][1] = 3; connectivity[2][2] = 6;
connectivity[3][0] = 3; connectivity[3][1] = 5; connectivity[3][2] = 6;
// LOCAL element orientations are always set so that they flow in the positive
// direction along an edge from node 0 to node 1. As a result if the GID of
// node 0 is larger then node 1 then the GLOBAL orientation is -1 (and positive
// otherwise. The local definition of the edge direction is defined by
// the shards cell topology.
{
std::vector<char> orientations(patternB->numberIds(),0);
orientation_helpers::computeCellEdgeOrientations(topEdgeIndices, connectivity[0], *patternB, orientations);
TEST_EQUALITY(orientations[0],char(1));
TEST_EQUALITY(orientations[1],char(-1));
TEST_EQUALITY(orientations[2],char(-1));
}
{
std::vector<char> orientations(patternB->numberIds(),0);
orientation_helpers::computeCellEdgeOrientations(topEdgeIndices, connectivity[1], *patternB, orientations);
TEST_EQUALITY(orientations[0],char(-1));
TEST_EQUALITY(orientations[1],char(1));
TEST_EQUALITY(orientations[2],char(1));
}
{
std::vector<char> orientations(patternB->numberIds(),0);
orientation_helpers::computeCellEdgeOrientations(topEdgeIndices, connectivity[2], *patternB, orientations);
TEST_EQUALITY(orientations[0],char(1));
TEST_EQUALITY(orientations[1],char(1));
TEST_EQUALITY(orientations[2],char(-1));
}
{
std::vector<char> orientations(patternB->numberIds(),0);
orientation_helpers::computeCellEdgeOrientations(topEdgeIndices, connectivity[3], *patternB, orientations);
TEST_EQUALITY(orientations[0],char(1));
TEST_EQUALITY(orientations[1],char(1));
TEST_EQUALITY(orientations[2],char(-1));
}
// lets now test an aggregate basis
std::vector<std::pair<int,Teuchos::RCP<const FieldPattern> > > patterns;
patterns.push_back(std::make_pair(0,patternB));
patterns.push_back(std::make_pair(1,patternC));
patterns.push_back(std::make_pair(2,patternA));
Teuchos::RCP<const FieldPattern> aggPattern = Teuchos::rcp(new FieldAggPattern(patterns));
std::vector<char> orientations(aggPattern->numberIds(),0);
orientation_helpers::computeCellEdgeOrientations(topEdgeIndices, connectivity[2], *aggPattern, orientations);
int nonzeroCount = 0;
for(std::size_t s=0;s<orientations.size();s++)
nonzeroCount += orientations[s]*orientations[s]; // should be +1 only if it is an edge
TEST_EQUALITY(nonzeroCount,6);
// loop over edges
char tests[] = { 1,1,-1}; // for element 2
for(std::size_t e=0;e<3;e++) {
const std::vector<int> & edgeIndices = aggPattern->getSubcellIndices(1,e);
for(std::size_t s=0;s<edgeIndices.size();s++)
TEST_EQUALITY(orientations[edgeIndices[s]],tests[e]);
}
}
DTKInterpolationAdapter::DTKInterpolationAdapter(Teuchos::RCP<const Teuchos::MpiComm<int> > in_comm, EquationSystems & in_es, const Point & offset, unsigned int from_dim):
comm(in_comm),
es(in_es),
_offset(offset),
mesh(in_es.get_mesh()),
dim(mesh.mesh_dimension())
{
MPI_Comm old_comm = Moose::swapLibMeshComm(*comm->getRawMpiComm());
std::set<GlobalOrdinal> semi_local_nodes;
get_semi_local_nodes(semi_local_nodes);
num_local_nodes = semi_local_nodes.size();
vertices.resize(num_local_nodes);
Teuchos::ArrayRCP<double> coordinates(num_local_nodes * dim);
Teuchos::ArrayRCP<double> target_coordinates(num_local_nodes * from_dim);
// Fill in the vertices and coordinates
{
GlobalOrdinal i = 0;
for (std::set<GlobalOrdinal>::iterator it = semi_local_nodes.begin();
it != semi_local_nodes.end();
++it)
{
const Node & node = mesh.node(*it);
vertices[i] = node.id();
for (GlobalOrdinal j=0; j<dim; j++)
coordinates[(j*num_local_nodes) + i] = node(j) + offset(j);
for (GlobalOrdinal j=0; j<from_dim; j++)
target_coordinates[(j*num_local_nodes) + i] = node(j) + offset(j);
i++;
}
}
// Currently assuming all elements are the same!
DataTransferKit::DTK_ElementTopology element_topology = get_element_topology(mesh.elem(0));
GlobalOrdinal n_nodes_per_elem = mesh.elem(0)->n_nodes();
GlobalOrdinal n_local_elem = mesh.n_local_elem();
elements.resize(n_local_elem);
Teuchos::ArrayRCP<GlobalOrdinal> connectivity(n_nodes_per_elem*n_local_elem);
Teuchos::ArrayRCP<double> elem_centroid_coordinates(n_local_elem*from_dim);
// Fill in the elements and connectivity
{
GlobalOrdinal i = 0;
MeshBase::const_element_iterator end = mesh.local_elements_end();
for (MeshBase::const_element_iterator it = mesh.local_elements_begin();
it != end;
++it)
{
const Elem & elem = *(*it);
elements[i] = elem.id();
for (GlobalOrdinal j=0; j<n_nodes_per_elem; j++)
connectivity[(j*n_local_elem)+i] = elem.node(j);
{
Point centroid = elem.centroid();
for (GlobalOrdinal j=0; j<from_dim; j++)
elem_centroid_coordinates[(j*n_local_elem) + i] = centroid(j) + offset(j);
}
i++;
}
}
Teuchos::ArrayRCP<int> permutation_list(n_nodes_per_elem);
for (GlobalOrdinal i = 0; i < n_nodes_per_elem; ++i )
permutation_list[i] = i;
/*
Moose::out<<"n_nodes_per_elem: "<<n_nodes_per_elem<<std::endl;
Moose::out<<"Dim: "<<dim<<std::endl;
Moose::err<<"Vertices size: "<<vertices.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Vertices: ";
for (unsigned int i=0; i<vertices.size(); i++)
Moose::err<<vertices[i]<<" ";
Moose::err<<std::endl;
}
Moose::err<<"Coordinates size: "<<coordinates.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Coordinates: ";
for (unsigned int i=0; i<coordinates.size(); i++)
Moose::err<<coordinates[i]<<" ";
Moose::err<<std::endl;
}
Moose::err<<"Connectivity size: "<<connectivity.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Connectivity: ";
for (unsigned int i=0; i<connectivity.size(); i++)
Moose::err<<connectivity[i]<<" ";
Moose::err<<std::endl;
}
Moose::err<<"Permutation_List size: "<<permutation_list.size()<<std::endl;
{
Moose::err<<libMesh::processor_id()<<" Permutation_List: ";
for (unsigned int i=0; i<permutation_list.size(); i++)
Moose::err<<permutation_list[i]<<" ";
Moose::err<<std::endl;
}
*/
Teuchos::RCP<MeshContainerType> mesh_container = Teuchos::rcp(
new MeshContainerType(dim, vertices, coordinates,
element_topology, n_nodes_per_elem,
elements, connectivity, permutation_list) );
// We only have 1 element topology in this grid so we make just one mesh block
Teuchos::ArrayRCP<Teuchos::RCP<MeshContainerType> > mesh_blocks(1);
mesh_blocks[0] = mesh_container;
// Create the MeshManager
mesh_manager = Teuchos::rcp(new DataTransferKit::MeshManager<MeshContainerType>(mesh_blocks, comm, dim) );
// Pack the coordinates into a field, this will be the positions we'll ask for other systems fields at
if (from_dim == dim)
target_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(mesh_container, comm));
else
{
Teuchos::ArrayRCP<GlobalOrdinal> empty_elements(0);
Teuchos::ArrayRCP<GlobalOrdinal> empty_connectivity(0);
Teuchos::RCP<MeshContainerType> coords_only_mesh_container = Teuchos::rcp(
new MeshContainerType(from_dim, vertices, target_coordinates,
element_topology, n_nodes_per_elem,
empty_elements, empty_connectivity, permutation_list) );
target_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(coords_only_mesh_container, comm));
}
{
Teuchos::ArrayRCP<GlobalOrdinal> empty_elements(0);
Teuchos::ArrayRCP<GlobalOrdinal> empty_connectivity(0);
Teuchos::RCP<MeshContainerType> centroid_coords_only_mesh_container = Teuchos::rcp(
new MeshContainerType(from_dim, elements, elem_centroid_coordinates,
element_topology, n_nodes_per_elem,
empty_elements, empty_connectivity, permutation_list) );
elem_centroid_coords = Teuchos::rcp(new DataTransferKit::FieldManager<MeshContainerType>(centroid_coords_only_mesh_container, comm));
}
// Swap back
Moose::swapLibMeshComm(old_comm);
}
vtkDataArray *
avtNodeDegreeExpression::DeriveVariable(vtkDataSet *in_ds)
{
vtkIdType nPoints = in_ds->GetNumberOfPoints();
// This is our connectivity list. It says that point P is connected to
// the points in connectivity[P]. A point is not connected to itself.
// Therefore, the degree of that node is connectivity[P].size().
// But first we have to construct the list.
std::vector<std::vector<int> > connectivity(nPoints);
vtkIdType nCells = in_ds->GetNumberOfCells();
for (vtkIdType i = 0 ; i < nCells ; i++)
{
vtkCell *cell = in_ds->GetCell(i);
vtkIdType numPointsForThisCell = cell->GetNumberOfPoints();
for (int localId = 0 ; localId < numPointsForThisCell ; localId++)
{
vtkIdType id = cell->GetPointId(localId);
// Most nodes have 3 adjacent nodes in that cell.
// One pryamid node has 4, and is treated as a special case.
// But we will store in adj[] the global ID of the points
// that this point is adjacent to.
int adj[4], nadj = 3;
switch (cell->GetCellType())
{
case VTK_TETRA:
switch (localId)
{
// Example reading:
// This first line says that
// CellLocalPointId 0 is adjacent to
// CellLocalPointIds 1,2 and 3. Please find what those
// point's global IDs are, and store them in adj[].
case 0: GlobalPointAssign(cell,adj,1,2,3); break;
case 1: GlobalPointAssign(cell,adj,0,2,3); break;
case 2: GlobalPointAssign(cell,adj,0,1,3); break;
case 3: GlobalPointAssign(cell,adj,0,1,2); break;
}
break;
case VTK_HEXAHEDRON:
switch (localId)
{
case 0: GlobalPointAssign(cell,adj,1,3,4); break;
case 1: GlobalPointAssign(cell,adj,0,2,5); break;
case 2: GlobalPointAssign(cell,adj,1,3,6); break;
case 3: GlobalPointAssign(cell,adj,0,2,7); break;
case 4: GlobalPointAssign(cell,adj,0,5,7); break;
case 5: GlobalPointAssign(cell,adj,1,4,6); break;
case 6: GlobalPointAssign(cell,adj,2,5,7); break;
case 7: GlobalPointAssign(cell,adj,3,4,6); break;
}
break;
case VTK_VOXEL:
switch (localId)
{
case 0: GlobalPointAssign(cell,adj,1,2,4); break;
case 1: GlobalPointAssign(cell,adj,0,3,5); break;
case 2: GlobalPointAssign(cell,adj,0,3,6); break;
case 3: GlobalPointAssign(cell,adj,1,2,7); break;
case 4: GlobalPointAssign(cell,adj,0,5,6); break;
case 5: GlobalPointAssign(cell,adj,1,4,7); break;
case 6: GlobalPointAssign(cell,adj,2,4,7); break;
case 7: GlobalPointAssign(cell,adj,3,5,6); break;
}
break;
case VTK_WEDGE:
switch (localId)
{
case 0: GlobalPointAssign(cell,adj,1,2,3); break;
case 1: GlobalPointAssign(cell,adj,0,2,4); break;
case 2: GlobalPointAssign(cell,adj,0,1,5); break;
case 3: GlobalPointAssign(cell,adj,0,4,5); break;
case 4: GlobalPointAssign(cell,adj,1,3,5); break;
case 5: GlobalPointAssign(cell,adj,2,3,4); break;
}
break;
case VTK_PYRAMID:
switch (localId)
{
case 0: GlobalPointAssign(cell,adj,1,3,4,-1); break;
case 1: GlobalPointAssign(cell,adj,0,2,4,-1); break;
case 2: GlobalPointAssign(cell,adj,1,3,4,-1); break;
case 3: GlobalPointAssign(cell,adj,0,2,4,-1); break;
case 4: GlobalPointAssign(cell,adj,0,1,2,3); nadj = 4; break;
}
break;
case VTK_QUAD:
nadj = 2;
switch (localId)
{
case 0: GlobalPointAssign2(cell,adj,1,3); break;
case 1: GlobalPointAssign2(cell,adj,0,2); break;
case 2: GlobalPointAssign2(cell,adj,1,3); break;
case 3: GlobalPointAssign2(cell,adj,0,2); break;
}
break;
case VTK_TRIANGLE:
nadj = 2;
switch (localId)
{
case 0: GlobalPointAssign2(cell,adj,1,2); break;
case 1: GlobalPointAssign2(cell,adj,0,2); break;
case 2: GlobalPointAssign2(cell,adj,0,1); break;
}
break;
case VTK_LINE:
nadj = 1;
switch (localId)
{
case 0: adj[0] = cell->GetPointId(1); break;
case 1: adj[0] = cell->GetPointId(0); break;
}
break;
default:
EXCEPTION0(ImproperUseException);
}
// Now we add to the connectivity list.
// Take the three points in adj[]
// and if they're not already in the connectivity list, add them.
for (int j = 0; j < nadj; j++)
{
if (VIntFind(connectivity[id],adj[j]) == -1)
connectivity[id].push_back(adj[j]);
}
}
}
//
// Set up a VTK variable reflecting the NodeDegrees we calculated, which
// is found by taking the length of the connectivity lists.
//
vtkIntArray *dv = vtkIntArray::New();
dv->SetNumberOfValues(nPoints);
for(vtkIdType i = 0 ; i < nPoints ; i++)
{
dv->SetValue(i, connectivity[i].size());
}
return dv;
}
