double compute_residual_norm2(fei::LinearSystem& fei_ls, fei::Vector& r)
{
fei::SharedPtr<fei::Matrix> A = fei_ls.getMatrix();
fei::SharedPtr<fei::Vector> x = fei_ls.getSolutionVector();
fei::SharedPtr<fei::Vector> b = fei_ls.getRHS();
//form r = A*x
A->multiply(x.get(), &r);
//form r = b - r (i.e., r = b - A*x)
r.update(1, b.get(), -1);
//!!!!!! fix this !!!!!!!!!
//terrible data copy. fei::Vector should provide a norm operation instead
//of making me roll my own here...
std::vector<int> indices;
r.getVectorSpace()->getIndices_Owned(indices);
std::vector<double> coefs(indices.size());
r.copyOut(indices.size(), &indices[0], &coefs[0]);
double local_sum = 0;
for(size_t i=0; i<indices.size(); ++i) {
local_sum += coefs[i]*coefs[i];
}
#ifdef HAVE_MPI
MPI_Comm comm = r.getVectorSpace()->getCommunicator();
double global_sum = 0;
int num_doubles = 1;
MPI_Allreduce(&local_sum, &global_sum, num_doubles, MPI_DOUBLE, MPI_SUM, comm);
#else
double global_sum = local_sum;
#endif
return std::sqrt(global_sum);
}
void copy_vector_to_mesh( fei::Vector & vec,
const DofMapper & dof,
stk_classic::mesh::BulkData & mesh_bulk_data
)
{
vec.scatterToOverlap();
std::vector<int> shared_and_owned_indices;
vec.getVectorSpace()->getIndices_SharedAndOwned(shared_and_owned_indices);
size_t num_values = shared_and_owned_indices.size();
if(num_values == 0) {
return;
}
std::vector<double> values(num_values);
vec.copyOut(num_values,&shared_and_owned_indices[0],&values[0]);
stk_classic::mesh::EntityRank ent_type;
stk_classic::mesh::EntityId ent_id;
const stk_classic::mesh::FieldBase * field;
int offset_into_field;
for(size_t i = 0; i < num_values; ++i)
{
dof.get_dof( shared_and_owned_indices[i],
ent_type,
ent_id,
field,
offset_into_field
);
stk_classic::mesh::Entity & entity = *mesh_bulk_data.get_entity(ent_type, ent_id);
void * data = stk_classic::mesh::field_data(*field,entity);
if(!(field->type_is<double>()) || data == NULL) {
std::ostringstream oss;
oss << "stk_classic::linsys::copy_vector_to_mesh ERROR, bad data type, or ";
oss << " field (" << field->name() << ") not found on entity with type " << entity.entity_rank();
oss << " and ID " << entity.identifier();
std::string str = oss.str();
throw std::runtime_error(str.c_str());
}
double * double_data = reinterpret_cast<double *>(data);
double_data[offset_into_field] = values[i];
}
}
bool confirm_vector_values(const fei::Vector& vec, double expected_value)
{
std::vector<int> indices;
fei::SharedPtr<fei::VectorSpace> vspace = vec.getVectorSpace();
vspace->getIndices_Owned(indices);
bool result = true;
if (indices.size() > 0) {
std::vector<double> coefs(indices.size());
vec.copyOut(indices.size(), &indices[0], &coefs[0]);
for(size_t i=0; i<indices.size(); ++i) {
if (std::abs(coefs[i] - expected_value) > 1.e-13) {
result = false;
break;
}
}
}
return result;
}
void scale_vector(double scalar,
fei::Vector& vec)
{
fei::SharedPtr<fei::VectorSpace> vspace = vec.getVectorSpace();
int numIndices = vspace->getNumIndices_Owned();
std::vector<int> indices(numIndices);
vspace->getIndices_Owned(numIndices, &indices[0], numIndices);
std::vector<double> coefs(numIndices);
vec.copyOut(numIndices, &indices[0], &coefs[0]);
for(size_t j=0; j<coefs.size(); ++j) {
coefs[j] *= scalar;
}
vec.copyIn(numIndices, &indices[0], &coefs[0]);
}
void add_vector_to_vector(double scalar,
const fei::Vector& src_vector,
fei::Vector& dest_vector)
{
fei::SharedPtr<fei::VectorSpace> vspace = src_vector.getVectorSpace();
int numIndices = vspace->getNumIndices_Owned();
std::vector<int> indices(numIndices);
vspace->getIndices_Owned(numIndices, &indices[0], numIndices);
std::vector<double> coefs(numIndices);
src_vector.copyOut(numIndices, &indices[0], &coefs[0]);
for(size_t j=0; j<coefs.size(); ++j) {
coefs[j] *= scalar;
}
dest_vector.sumIn(numIndices, &indices[0], &coefs[0]);
}
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]);
}
}
}