typename stk_classic::mesh::FieldTraits<field_type>::data_type
dot( const stk_classic::AlgorithmRunnerInterface & alg_runner ,
const stk_classic::mesh::BulkData& bulk,
const stk_classic::mesh::EntityRank entitytype,
const field_type & x ,
const field_type & y )
{
// Construct algorithm to hand to local parallel algorithm runner
DotAlg<field_type> alg_dot(x,y);
const std::vector<stk_classic::mesh::Bucket*>
& all_entity_buckets = bulk.buckets( entitytype );
stk_classic::mesh::Selector
select_owned( stk_classic::mesh::MetaData::get(bulk).locally_owned_part());
double local_dot = 0 ;
double global_dot = 0 ;
// Local parallel execution of the algorithm
stk_classic::mesh::PartVector empty_union_vector;
alg_runner.run( select_owned , empty_union_vector, all_entity_buckets , alg_dot , & local_dot );
// Global sum
#if defined( STK_HAS_MPI )
MPI_Comm comm = bulk.parallel();
MPI_Allreduce(& local_dot , & global_dot, 1, MPI_DOUBLE, MPI_SUM, comm);
#else
global_dot = local_dot;
#endif
return global_dot ;
}
bool use_case_5_driver( MPI_Comm comm ,
const std::string& mesh_options,
const std::string& solver_params )
{
if ( 0 == stk::parallel_machine_rank( comm ) ) {
std::cout << "stk_linsys use case 5" << std::endl
<< " Number Processes = " << stk::parallel_machine_size( comm )
<< std::endl ;
}
//--------------------------------------------------------------------
{
//------------------------------------------------------------------
// Declare the mesh meta data: element blocks and associated fields
stk::mesh::fem::FEMMetaData fem_meta(SpatialDim, stk::mesh::fem::entity_rank_names(SpatialDim) ) ;
Ioss::Init::Initializer init_db;
stk::mesh::MetaData & mesh_meta_data = stk::mesh::fem::FEMMetaData::get_meta_data(fem_meta);
{
const stk::mesh::fem::FEMMetaData &fmd = fem_meta.get ( mesh_meta_data );
std::cout <<fmd.is_FEM_initialized()<<endl;
}
const stk::mesh::EntityRank element_rank = fem_meta.element_rank();
//--------------------------------
// Element-block declarations typically occur when reading the
// mesh-file meta-data, and thus won't usually appear in application code.
// Declaring the element blocks and associating an element traits
// with each element block.
stk::mesh::Part & universal = fem_meta.universal_part();
stk::mesh::Part & block_hex = fem_meta.declare_part("block_1", element_rank);
stk::mesh::Part & block_quad_shell = fem_meta.declare_part("block_2", element_rank);
stk::mesh::fem::CellTopology hex_top(shards::getCellTopologyData<shards::Hexahedron<> >());
stk::mesh::fem::CellTopology qshell_top(shards::getCellTopologyData<shards::ShellQuadrilateral<> >());
stk::mesh::fem::set_cell_topology( block_hex, hex_top );
stk::mesh::fem::set_cell_topology( block_quad_shell, qshell_top );
stk::io::put_io_part_attribute(block_hex);
stk::io::put_io_part_attribute(block_quad_shell);
//--------------------------------
// Declaring fields of specified types on all nodes:
VectorFieldType & coordinates_field =
stk::mesh::put_field(
fem_meta.declare_field< VectorFieldType >( "coordinates" ) ,
stk::mesh::fem::FEMMetaData::NODE_RANK , universal , SpatialDim );
VectorFieldType & displacements_field =
stk::mesh::put_field(
fem_meta.declare_field< VectorFieldType >( "displacements" ) ,
stk::mesh::fem::FEMMetaData::NODE_RANK , universal , SpatialDim );
//--------------------------------
// rotation_field only exists on the shell-nodes:
VectorFieldType & rotation_field =
stk::mesh::put_field(
fem_meta.declare_field< VectorFieldType >( "rotation" ),
stk::mesh::fem::FEMMetaData::NODE_RANK , block_quad_shell , SpatialDim );
stk::mesh::Part& bcpart = fem_meta.declare_part("bcpart");
// Define the transient fields that will be output.
stk::io::set_field_role(displacements_field, Ioss::Field::TRANSIENT);
//--------------------------------
// Commit (finalize) the meta data. Is now ready to be used
// in the creation and management of mesh bulk data.
fem_meta.commit();
//------------------------------------------------------------------
// stk::mesh::BulkData bulk data conforming to the meta data.
stk::mesh::BulkData mesh_bulk_data( mesh_meta_data , comm );
// In a typical app, the mesh would be read from file at this point.
// But in this use-case, we generate the mesh and initialize
// field data to use-case defined values.
use_case_5_generate_mesh(
mesh_options ,
mesh_bulk_data ,
coordinates_field ,
block_hex ,
block_quad_shell );
use_case_5_initialize_data(
mesh_bulk_data ,
coordinates_field ,
displacements_field ,
rotation_field );
//Add a node to our boundary-condition part 'bcpart'.
//let's choose the first locally-owned node. (This will produce a
//different boundary-condition for different numbers of processors...
//A more realistic case would simply pick a specific set of nodes
//regardless of which processors they are on.)
mesh_bulk_data.modification_begin();
std::vector<stk::mesh::Entity*> local_nodes;
stk::mesh::Selector select_owned(fem_meta.locally_owned_part());
stk::mesh::get_selected_entities(select_owned,
mesh_bulk_data.buckets(stk::mesh::fem::FEMMetaData::NODE_RANK),
local_nodes);
if (local_nodes.size() > 0) {
stk::mesh::PartVector partvector;
partvector.push_back(&bcpart);
mesh_bulk_data.change_entity_parts(*local_nodes[0], partvector);
}
mesh_bulk_data.modification_end();
//set owner-processors to lowest-sharing (stk::mesh defaults to
//highest-sharing) If highest-sharing owns, then it isn't correct for the
//way the fei library sets ownership of shared nodes for vectors etc.
stk::mesh::set_owners<stk::mesh::LowestRankSharingProcOwns>( mesh_bulk_data );
//Note: set_owners should throw an error if not done inside a modification_begin/end block.
//------------------------------------------------------------------
const unsigned myProc = mesh_bulk_data.parallel_rank();
//Now begin the use-case:
//Create a fei::Factory of type Factory_Trilinos, which will produce
//fei::Matrix and fei::Vector objects with run-time-type compatible with Trilinos.
fei::SharedPtr<fei::Factory> feifactory(new Factory_Trilinos(comm));
stk::linsys::LinearSystem ls(comm, feifactory);
if (myProc == 0) {
std::cout << "Adding element-node connectivities for displacements field for all locally-owned "
<< "elements..." << std::endl;
}
//Add connectivities for our mesh to the linsys::LinearSystem object. This
//will enable us to generate a matrix-graph:
stk::linsys::add_connectivities(ls, element_rank,
stk::mesh::fem::FEMMetaData::NODE_RANK,
displacements_field, select_owned, mesh_bulk_data);
ls.synchronize_mappings_and_structure();
ls.create_fei_LinearSystem();
fei::SharedPtr<fei::MatrixGraph> matgraph = ls.get_fei_MatrixGraph();
fei::SharedPtr<fei::Matrix> matrix = ls.get_fei_LinearSystem()->getMatrix();
fei::SharedPtr<fei::Vector> rhs = ls.get_fei_LinearSystem()->getRHS();
fei::SharedPtr<fei::Vector> solution = ls.get_fei_LinearSystem()->getSolutionVector();
//Now we'll run through the mesh and load up dense element-matrices and element-vectors
//to assemble into the global sparse linear-system:
{
const std::vector<stk::mesh::Bucket*>& mesh_buckets = mesh_bulk_data.buckets(element_rank);
std::vector<stk::mesh::Bucket*> part_buckets;
stk::mesh::get_buckets(select_owned, mesh_buckets, part_buckets);
stk::linsys::DofMapper& dof_mapper = ls.get_DofMapper();
int field_id = dof_mapper.get_field_id(displacements_field);
stk::mesh::Entity& first_entity = *(part_buckets[0]->begin());
stk::mesh::PairIterRelation rel = first_entity.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
int num_nodes_per_elem = rel.second - rel.first;
int pattern_id = matgraph->definePattern(num_nodes_per_elem, stk::mesh::fem::FEMMetaData::NODE_RANK, field_id);
std::vector<int> node_ids(num_nodes_per_elem);
const int field_size = dof_mapper.get_fei_VectorSpace()->getFieldSize(field_id);
const int matsize = num_nodes_per_elem*field_size*num_nodes_per_elem*field_size;
const int vecsize = num_nodes_per_elem*field_size;
std::vector<double> elem_matrix_1d(matsize, 0);
std::vector<double*> elem_matrix_2d(vecsize);
std::vector<double> elem_vector(vecsize, 0);
for(size_t i=0; i<elem_matrix_2d.size(); ++i) {
elem_matrix_2d[i] = &elem_matrix_1d[i*vecsize];
}
//fill our dummy elem-matrix:
//This dummy matrix will be the same for every element. A real application
//would form a different elem-matrix for each element.
for(size_t i=0; i<elem_matrix_2d.size(); ++i) {
double* row = elem_matrix_2d[i];
if (i>=1) row[i-1] = -1;
row[i] = 2;
if (i<elem_matrix_2d.size()-1) row[i+1] = -1;
elem_vector[i] = 1;
}
std::vector<int> eqn_indices(vecsize);
for(size_t i=0; i<part_buckets.size(); ++i) {
stk::mesh::Bucket::iterator
b_iter = part_buckets[i]->begin(),
b_end = part_buckets[i]->end();
for(; b_iter != b_end; ++b_iter) {
stk::mesh::Entity& elem = *b_iter;
rel = elem.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
for(int j=0; rel.first != rel.second; ++rel.first, ++j) {
node_ids[j] = rel.first->entity()->identifier();
}
matgraph->getPatternIndices(pattern_id, &node_ids[0], eqn_indices);
matrix->sumIn(vecsize, &eqn_indices[0], vecsize, &eqn_indices[0],
&elem_matrix_2d[0]);
rhs->sumIn(vecsize, &eqn_indices[0], &elem_vector[0]);
}
}
stk::linsys::dirichlet_bc(ls, mesh_bulk_data, bcpart, stk::mesh::fem::FEMMetaData::NODE_RANK,
displacements_field, 0, 3.14159265);
ls.finalize_assembly();
//Read solver-parameters out of a file. In a real application this would
//be done during a parsing phase, *not* here in the assembly code.
Teuchos::ParameterList params;
if (solver_params != "") {
Teuchos::ParameterXMLFileReader param_file(solver_params);
params = param_file.getParameters();
}
//Launch the linear-solver:
int status = 0, ret;
ret = ls.solve(status, params);
if (ret != 0) {
throw std::runtime_error("Error in the linear solver.");
}
//Copy the contents of the solution-vector back into our mesh-data:
copy_vector_to_mesh( *solution, dof_mapper, mesh_bulk_data);
}
//This following section writes mesh data out to an exodus file:
{
const std::string out_filename("mesh.e");
stk::io::MeshData mesh;
stk::io::create_output_mesh(out_filename, comm, mesh_bulk_data, mesh);
stk::io::define_output_fields(mesh, fem_meta);
// Write the model to the mesh file (topology, coordinates, attributes, etc)
stk::io::process_output_request(mesh, mesh_bulk_data, 0.0);
}
//Write out our assembled linear-system to files:
matrix->writeToFile("A.mtx");
rhs->writeToFile("rhs.vec");
solution->writeToFile("solution.vec");
}
return true;
}
STKUNIT_UNIT_TEST(UnitTestLinsysFunctions, test1)
{
static const size_t spatial_dimension = 3;
MPI_Barrier( MPI_COMM_WORLD );
MPI_Comm comm = MPI_COMM_WORLD;
//First create and fill MetaData and BulkData objects:
const unsigned bucket_size = 100; //for a real application mesh, bucket_size would be much bigger...
stk::mesh::fem::FEMMetaData fem_meta;
stk::mesh::fem::FEMMetaData fem_meta2;
fem_meta.FEM_initialize(spatial_dimension);
fem_meta2.FEM_initialize(spatial_dimension);
stk::mesh::MetaData & meta_data = stk::mesh::fem::FEMMetaData::get_meta_data(fem_meta);
stk::mesh::MetaData & meta_data2 = stk::mesh::fem::FEMMetaData::get_meta_data(fem_meta2);
const stk::mesh::EntityRank element_rank = fem_meta.element_rank();
stk::mesh::BulkData bulk_data( meta_data, comm, bucket_size );
stk::mesh::BulkData bulk_data2( meta_data2, comm, bucket_size );
//create a boundary-condition part for testing later:
stk::mesh::Part& bcpart = fem_meta.declare_part("bcpart");
fill_utest_mesh_meta_data( fem_meta );
bool use_temperature=false;
fill_utest_mesh_meta_data( fem_meta2, use_temperature );
fill_utest_mesh_bulk_data( bulk_data );
fill_utest_mesh_bulk_data( bulk_data2 );
//set owner-processors to lowest-sharing (stk::mesh defaults to
//highest-sharing) If highest-sharing owns, then it isn't correct for the
//way the fei library sets ownership of shared nodes for vectors etc.
stk::mesh::set_owners<stk::mesh::LowestRankSharingProcOwns>( bulk_data );
//put a node in our boundary-condition part. arbitrarily choose the
//first locally-owned node:
bulk_data.modification_begin();
std::vector<stk::mesh::Entity*> local_nodes;
stk::mesh::Selector select_owned(meta_data.locally_owned_part());
stk::mesh::get_selected_entities(select_owned,
bulk_data.buckets(NODE_RANK),
local_nodes);
stk::mesh::EntityId bc_node_id = 0;
if (local_nodes.size() > 0) {
stk::mesh::PartVector partvector;
partvector.push_back(&bcpart);
bulk_data.change_entity_parts(*local_nodes[0], partvector);
bc_node_id = stk::linsys::impl::entityid_to_int(local_nodes[0]->identifier());
}
bulk_data.modification_end();
stk::mesh::Selector selector = ( meta_data.locally_owned_part() | meta_data.globally_shared_part() ) & *meta_data.get_part("block_1");
std::vector<unsigned> count;
stk::mesh::count_entities(selector, bulk_data, count);
STKUNIT_ASSERT_EQUAL( count[element_rank], (unsigned)4 );
STKUNIT_ASSERT_EQUAL( count[NODE_RANK], (unsigned)20 );
ScalarField* temperature_field = meta_data.get_field<ScalarField>("temperature");
//Create a fei Factory and stk::linsys::LinearSystem object:
fei::SharedPtr<fei::Factory> factory(new Factory_Trilinos(comm));
stk::linsys::LinearSystem ls(comm, factory);
stk::linsys::add_connectivities(ls, element_rank, NODE_RANK,
*temperature_field, selector, bulk_data);
fei::SharedPtr<fei::MatrixGraph> matgraph = ls.get_fei_MatrixGraph();
int num_blocks = matgraph->getNumConnectivityBlocks();
STKUNIT_ASSERT_EQUAL( num_blocks, (int)1 );
ls.synchronize_mappings_and_structure();
ls.create_fei_LinearSystem();
//put 0 throughout the matrix and 3 throughout the rhs:
fei::SharedPtr<fei::Matrix> mat = ls.get_fei_LinearSystem()->getMatrix();
ls.get_fei_LinearSystem()->getMatrix()->putScalar(0);
ls.get_fei_LinearSystem()->getRHS()->putScalar(3.0);
//put 10 on the matrix diagonal to ensure it will be easy to solve later.
fei::SharedPtr<fei::VectorSpace> vspace = ls.get_fei_LinearSystem()->getRHS()->getVectorSpace();
int numLocalRows = vspace->getNumIndices_Owned();
std::vector<int> local_rows(numLocalRows);
vspace->getIndices_Owned(numLocalRows, &local_rows[0], numLocalRows);
for(size_t i=0; i<local_rows.size(); ++i) {
int col = local_rows[i];
double coef = 10;
double* coefPtr = &coef;
mat->sumIn(1, &local_rows[i], 1, &col, &coefPtr);
}
//now we'll impose a dirichlet bc on our one-node bcpart:
stk::linsys::dirichlet_bc(ls, bulk_data, bcpart, NODE_RANK,
*temperature_field, 0, 9.0);
ls.finalize_assembly();
//now confirm that the rhs value for the equation corresponding to our
//bc node is 9.0:
fei::SharedPtr<fei::Vector> rhsvec = ls.get_fei_LinearSystem()->getRHS();
double rhs_bc_val = 0;
int bc_eqn_index = ls.get_DofMapper().get_global_index(NODE_RANK,
bc_node_id, *temperature_field);
rhsvec->copyOut(1, &bc_eqn_index, &rhs_bc_val);
bool bc_val_is_correct = std::abs(rhs_bc_val - 9.0) < 1.e-13;
STKUNIT_ASSERT( bc_val_is_correct );
stk::linsys::copy_vector_to_mesh( *rhsvec, ls.get_DofMapper(), bulk_data);
stk::mesh::Entity* bc_node = bulk_data.get_entity(NODE_RANK, local_nodes[0]->identifier());
stk::mesh::FieldTraits<ScalarField>::data_type* bc_node_data = stk::mesh::field_data(*temperature_field, *bc_node);
bool bc_node_data_is_correct = std::abs(bc_node_data[0] - 9.0) < 1.e-13;
STKUNIT_ASSERT( bc_node_data_is_correct );
//now make sure we get a throw if we use the wrong bulk-data (that doesn't have the
//temperature field defined)
STKUNIT_ASSERT_THROW(stk::linsys::copy_vector_to_mesh( *rhsvec, ls.get_DofMapper(), bulk_data2), std::runtime_error);
//obtain and zero the solution vector
fei::SharedPtr<fei::Vector> solnvec = ls.get_fei_LinearSystem()->getSolutionVector();
solnvec->putScalar(0);
//copy the vector of zeros into the mesh:
stk::linsys::copy_vector_to_mesh( *solnvec, ls.get_DofMapper(), bulk_data);
//assert that our bc node's data is now zero.
bc_node_data_is_correct = std::abs(bc_node_data[0] - 0) < 1.e-13;
STKUNIT_ASSERT( bc_node_data_is_correct );
//call the linear-system solve function.
//(note that when we add options to the solve method, we'll need to enhance this
//testing to exercise various specific solves.)
Teuchos::ParameterList params;
int status = 0;
ls.solve(status, params);
//copy the solution-vector into the mesh:
stk::linsys::copy_vector_to_mesh( *solnvec, ls.get_DofMapper(), bulk_data);
//now assert that the value 9 (bc value) produced by the solve is in this
//node's data.
//note that we use a loose tolerance, because the default solver tolerance
//is (I think) only 1.e-6.
bc_node_data_is_correct = std::abs(bc_node_data[0] - 9.0) < 1.e-6;
STKUNIT_ASSERT( bc_node_data_is_correct );
STKUNIT_ASSERT(bc_node_data_is_correct);
}
void UnitTestBulkData::testChangeParts_loop( ParallelMachine pm )
{
enum { nPerProc = 10 };
const unsigned p_rank = parallel_machine_rank( pm );
const unsigned p_size = parallel_machine_size( pm );
const unsigned nLocalNode = nPerProc + ( 1 < p_size ? 1 : 0 );
const unsigned nLocalEdge = nPerProc ;
UnitTestRingMeshFixture ring_mesh( pm , nPerProc , true /* generate parts */ );
ring_mesh.m_meta_data.commit();
ring_mesh.generate_mesh( false /* no aura */ );
Part & part_owns = ring_mesh.m_meta_data.locally_owned_part();
Part & part_univ = ring_mesh.m_meta_data.universal_part();
Selector select_owned( ring_mesh.m_meta_data.locally_owned_part() );
Selector select_used = select_owned | ring_mesh.m_meta_data.globally_shared_part();
Selector select_all( ring_mesh.m_meta_data.universal_part() );
std::vector<unsigned> local_count ;
for ( unsigned i = 0 ; i < nLocalEdge ; ++i ) {
const unsigned n = i + nPerProc * p_rank ;
Entity * const edge = ring_mesh.m_bulk_data.get_entity( 1 , ring_mesh.m_edge_ids[n] );
STKUNIT_ASSERT( edge != NULL );
STKUNIT_ASSERT( edge->bucket().member( part_univ ) );
STKUNIT_ASSERT( edge->bucket().member( part_owns ) );
STKUNIT_ASSERT( edge->bucket().member( * ring_mesh.m_edge_parts[ n % ring_mesh.m_edge_parts.size() ] ) );
}
for ( unsigned i = 0 ; i < nLocalNode ; ++i ) {
const unsigned n = ( i + nPerProc * p_rank ) % ring_mesh.m_node_ids.size();
const unsigned e0 = n ;
const unsigned e1 = ( n + ring_mesh.m_edge_ids.size() - 1 ) % ring_mesh.m_edge_ids.size();
const unsigned ns = ring_mesh.m_edge_parts.size();
const unsigned n0 = e0 % ns ;
const unsigned n1 = e1 % ns ;
Part * const epart_0 = ring_mesh.m_edge_parts[ n0 < n1 ? n0 : n1 ];
Part * const epart_1 = ring_mesh.m_edge_parts[ n0 < n1 ? n1 : n0 ];
Entity * const node = ring_mesh.m_bulk_data.get_entity( 0 , ring_mesh.m_node_ids[n] );
STKUNIT_ASSERT( node != NULL );
if ( node->owner_rank() == p_rank ) {
STKUNIT_ASSERT( node->bucket().member( part_univ ) );
STKUNIT_ASSERT( node->bucket().member( part_owns ) );
STKUNIT_ASSERT( node->bucket().member( *epart_0 ) );
STKUNIT_ASSERT( node->bucket().member( *epart_1 ) );
}
else {
STKUNIT_ASSERT( node->bucket().member( part_univ ) );
STKUNIT_ASSERT( ! node->bucket().member( part_owns ) );
STKUNIT_ASSERT( node->bucket().member( * epart_0 ) );
STKUNIT_ASSERT( node->bucket().member( * epart_1 ) );
}
}
ring_mesh.m_bulk_data.modification_begin();
if ( 0 == p_rank ) {
for ( unsigned i = 0 ; i < nLocalEdge ; ++i ) {
const unsigned n = i + nPerProc * p_rank ;
PartVector add(1); add[0] = & ring_mesh.m_edge_part_extra ;
PartVector rem(1); rem[0] = ring_mesh.m_edge_parts[ n % ring_mesh.m_edge_parts.size() ];
Entity * const edge = ring_mesh.m_bulk_data.get_entity( 1 , ring_mesh.m_edge_ids[n] );
ring_mesh.m_bulk_data.change_entity_parts( *edge , add , rem );
STKUNIT_ASSERT( edge->bucket().member( part_univ ) );
STKUNIT_ASSERT( edge->bucket().member( part_owns ) );
STKUNIT_ASSERT( edge->bucket().member(ring_mesh.m_edge_part_extra ) );
}
}
ring_mesh.m_bulk_data.modification_end();
for ( unsigned i = 0 ; i < nLocalNode ; ++i ) {
const unsigned n = ( i + nPerProc * p_rank ) % ring_mesh.m_node_ids.size();
const unsigned e0 = n ;
const unsigned e1 = ( n + ring_mesh.m_edge_ids.size() - 1 ) % ring_mesh.m_edge_ids.size();
const unsigned ns = ring_mesh.m_edge_parts.size();
const unsigned n0 = e0 % ns ;
const unsigned n1 = e1 % ns ;
Part * ep_0 = e0 < nLocalEdge ? & ring_mesh.m_edge_part_extra : ring_mesh.m_edge_parts[n0] ;
Part * ep_1 = e1 < nLocalEdge ? & ring_mesh.m_edge_part_extra : ring_mesh.m_edge_parts[n1] ;
Part * epart_0 = ep_0->mesh_meta_data_ordinal() < ep_1->mesh_meta_data_ordinal() ? ep_0 : ep_1 ;
Part * epart_1 = ep_0->mesh_meta_data_ordinal() < ep_1->mesh_meta_data_ordinal() ? ep_1 : ep_0 ;
Entity * const node = ring_mesh.m_bulk_data.get_entity( 0 , ring_mesh.m_node_ids[n] );
STKUNIT_ASSERT( node != NULL );
if ( node->owner_rank() == p_rank ) {
STKUNIT_ASSERT( node->bucket().member( part_owns ) );
}
else {
STKUNIT_ASSERT( ! node->bucket().member( part_owns ) );
}
STKUNIT_ASSERT( node->bucket().member( part_univ ) );
STKUNIT_ASSERT( node->bucket().member( *epart_0 ) );
STKUNIT_ASSERT( node->bucket().member( *epart_1 ) );
}
}
void assemble_elem_matrices_and_vectors(stk::mesh::BulkData& mesh,
stk::mesh::FieldBase& field,
stk::linsys::DofMapper& dof_mapper,
fei::Matrix& matrix,
fei::Vector& rhs)
{
stk::mesh::fem::FEMMetaData &fem = stk::mesh::fem::FEMMetaData::get(mesh);
const stk::mesh::EntityRank element_rank = fem.element_rank();
const std::vector<stk::mesh::Bucket*>& mesh_buckets = mesh.buckets(element_rank);
std::vector<stk::mesh::Bucket*> part_buckets;
stk::mesh::Selector select_owned(stk::mesh::MetaData::get(mesh).locally_owned_part());
stk::mesh::get_buckets(select_owned, mesh_buckets, part_buckets);
int field_id = dof_mapper.get_field_id(field);
stk::mesh::Entity& first_entity = *(part_buckets[0]->begin());
stk::mesh::PairIterRelation rel = first_entity.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
int num_nodes_per_elem = rel.second - rel.first;
fei::SharedPtr<fei::MatrixGraph> matgraph = matrix.getMatrixGraph();
int pattern_id = matgraph->definePattern(num_nodes_per_elem, stk::mesh::fem::FEMMetaData::NODE_RANK, field_id);
std::vector<int> node_ids(num_nodes_per_elem);
const int field_size = dof_mapper.get_fei_VectorSpace()->getFieldSize(field_id);
const int matsize = num_nodes_per_elem*field_size*num_nodes_per_elem*field_size;
const int vecsize = num_nodes_per_elem*field_size;
std::vector<double> elem_matrix_1d(matsize, 0);
std::vector<double*> elem_matrix_2d(vecsize);
std::vector<double> elem_vector(vecsize, 0);
for(size_t i=0; i<elem_matrix_2d.size(); ++i) {
elem_matrix_2d[i] = &elem_matrix_1d[i*vecsize];
}
//fill our dummy elem-matrix:
//This dummy matrix will be the same for every element. A real application
//would form a different elem-matrix for each element.
for(size_t i=0; i<elem_matrix_2d.size(); ++i) {
double* row = elem_matrix_2d[i];
if (i>=1) row[i-1] = -1;
row[i] = 2;
if (i<elem_matrix_2d.size()-1) row[i+1] = -1;
elem_vector[i] = 1;
}
std::vector<int> eqn_indices(vecsize);
for(size_t i=0; i<part_buckets.size(); ++i) {
stk::mesh::Bucket::iterator
b_iter = part_buckets[i]->begin(),
b_end = part_buckets[i]->end();
for(; b_iter != b_end; ++b_iter) {
stk::mesh::Entity& elem = *b_iter;
rel = elem.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
for(int j=0; rel.first != rel.second; ++rel.first, ++j) {
node_ids[j] = rel.first->entity()->identifier();
}
matgraph->getPatternIndices(pattern_id, &node_ids[0], eqn_indices);
matrix.sumIn(vecsize, &eqn_indices[0], vecsize, &eqn_indices[0],
&elem_matrix_2d[0]);
rhs.sumIn(vecsize, &eqn_indices[0], &elem_vector[0]);
}
}
}
