void interp_nodal_hessian(
const int hess_id,
PerceptMesh& eMesh,
VectorFieldType* nodal_hessian_field)
{
const int spatial_dim = eMesh.get_spatial_dim();
stk::mesh::Selector selector =
eMesh.get_fem_meta_data()->locally_owned_part() |
eMesh.get_fem_meta_data()->globally_shared_part();
std::vector<stk::mesh::Bucket*> buckets;
stk::mesh::get_buckets( selector, eMesh.get_bulk_data()->buckets( eMesh.node_rank() ), buckets );
for ( vector<stk::mesh::Bucket*>::const_iterator k = buckets.begin() ; k != buckets.end() ; ++k ) {
stk::mesh::Bucket & bucket = **k ;
const unsigned num_nodes_in_bucket = bucket.size();
for (unsigned i = 0; i < num_nodes_in_bucket; i++) {
stk::mesh::Entity& node = bucket[i];
const double *coords = stk::mesh::field_data( *eMesh.get_coordinates_field() , node);
double *hess = stk::mesh::field_data( *nodal_hessian_field , node);
exact_hessian(hess_id, coords, hess, spatial_dim);
}
}
}
void PMMParallelReferenceMeshSmoother::run_wrapper( Mesh* mesh,
ParallelMesh* pmesh,
MeshDomain* domain,
Settings* settings,
QualityAssessor* qa,
MsqError& err )
{
std::cout << "\nP[" << Mesquite::get_parallel_rank() << "] tmp srk PMMParallelReferenceMeshSmoother innerIter= " << innerIter << " parallelIterations= " << parallelIterations << std::endl;
//if (!get_parallel_rank())
std::cout << "\nP[" << get_parallel_rank() << "] tmp srk PMMParallelReferenceMeshSmoother: running shape improver... \n" << std::endl;
PerceptMesquiteMesh *pmm = dynamic_cast<PerceptMesquiteMesh *>(mesh);
PerceptMesh *eMesh = pmm->getPerceptMesh();
m_pmm= pmm;
m_eMesh = eMesh;
m_num_nodes = m_eMesh->get_number_nodes();
print_comm_list(*eMesh->get_bulk_data(), false);
stk::mesh::FieldBase *coord_field = eMesh->get_coordinates_field();
stk::mesh::FieldBase *coord_field_current = coord_field;
stk::mesh::FieldBase *coord_field_projected = eMesh->get_field("coordinates_N");
stk::mesh::FieldBase *coord_field_original = eMesh->get_field("coordinates_NM1");
stk::mesh::FieldBase *coord_field_lagged = eMesh->get_field("coordinates_lagged");
m_coord_field_original = coord_field_original;
m_coord_field_projected = coord_field_projected;
m_coord_field_lagged = coord_field_lagged;
m_coord_field_current = coord_field_current;
eMesh->copy_field(coord_field_lagged, coord_field_original);
// untangle
PMMSmootherMetricUntangle untangle_metric(eMesh);
// shape-size-orient smooth
PMMSmootherMetricShapeSizeOrient shape_metric(eMesh);
// shape
PMMSmootherMetricShapeB1 shape_b1_metric(eMesh);
// scaled jacobian
PMMSmootherMetricScaledJacobianElemental scaled_jac_metric(eMesh);
// scaled jacobian - nodal
PMMSmootherMetricScaledJacobianNodal scaled_jac_metric_nodal(eMesh);
//double omegas[] = {0.0, 0.001, 0.01, 0.1, 0.2, 0.4, 0.6, 0.8, 1.0};
//double omegas[] = {0.001, 1.0};
//double omegas[] = { 0.001, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.4, 0.45,0.46,0.47,0.48,0.49,0.5,0.52,0.54,0.56,0.59, 0.6, 0.8, 1.0};
double omegas[] = { 1.0};
//double omegas[] = {0.0, 0.001, 0.01, 0.1, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.2, 0.4, 0.6, 0.8, 1.0};
int nomega = sizeof(omegas)/sizeof(omegas[0]);
for (int outer = 0; outer < nomega; outer++)
{
double omega = (outer < nomega ? omegas[outer] : 1.0);
m_omega = omega;
m_omega_prev = omega;
if (outer > 0) m_omega_prev = omegas[outer-1];
// set current state and evaluate mesh validity (current = omega*project + (1-omega)*original)
eMesh->nodal_field_axpbypgz(omega, coord_field_projected, (1.0-omega), coord_field_original, 0.0, coord_field_current);
int num_invalid = PMMParallelShapeImprover::parallel_count_invalid_elements(m_eMesh);
if (!get_parallel_rank())
std::cout << "\ntmp srk PMMParallelReferenceMeshSmoother num_invalid current= " << num_invalid << " for outer_iter= " << outer
<< " omega= " << omega
<< (num_invalid ? " WARNING: invalid elements exist before Mesquite smoothing" : " OK")
<< std::endl;
//if (num_invalid) return;
m_num_invalid = num_invalid;
m_untangled = (m_num_invalid == 0);
int iter_all=0;
int do_anim = 0; // = frequency of anim writes
if (do_anim)
{
eMesh->save_as("anim_all."+toString(iter_all)+".e");
}
for (int stage = 0; stage < 2; stage++)
{
m_stage = stage;
if (stage==0)
{
m_metric = &untangle_metric;
//m_metric = &scaled_jac_metric_nodal;
}
else
{
int num_invalid_1 = PMMParallelShapeImprover::parallel_count_invalid_elements(m_eMesh);
VERIFY_OP_ON(num_invalid_1, ==, 0, "Invalid elements exist for start of stage 2, aborting");
//m_metric = &shape_metric;
m_metric = &shape_b1_metric;
//m_metric = &scaled_jac_metric;
}
for (int iter = 0; iter < innerIter; ++iter, ++iter_all)
{
m_iter = iter;
int num_invalid_0 = PMMParallelShapeImprover::parallel_count_invalid_elements(m_eMesh);
m_num_invalid = num_invalid_0;
// if (!get_parallel_rank() && num_invalid_0)
// std::cout << "\ntmp srk PMMParallelReferenceMeshSmoother num_invalid current= " << num_invalid_0
// << (num_invalid ? " WARNING: invalid elements exist before Mesquite smoothing" : "OK")
// << std::endl;
m_global_metric = run_one_iteration(mesh, domain, err);
sync_fields(iter);
num_invalid_0 = PMMParallelShapeImprover::parallel_count_invalid_elements(m_eMesh);
m_num_invalid = num_invalid_0;
bool conv = check_convergence();
if (!get_parallel_rank())
{
std::cout << "P[" << get_parallel_rank() << "] " << "tmp srk iter= " << iter << " dmax= " << m_dmax << " m_dnew= " << m_dnew
<< " m_d0= " << m_d0 << " m_alpha= " << m_alpha << " m_grad_norm= " << m_grad_norm << " m_scaled_grad_norm = " << m_scaled_grad_norm
<< " num_invalid= " << num_invalid_0
<< " m_global_metric= " << m_global_metric << " m_untangled= " << m_untangled
<< std::endl;
}
if (do_anim)
{
eMesh->save_as("iter_"+toString(outer)+"_"+toString(stage)+"."+toString(iter+1)+".e");
if (iter_all % do_anim == 0) eMesh->save_as("anim_all."+toString(iter_all+1)+".e");
}
if (!m_untangled && m_num_invalid == 0)
{
m_untangled = true;
}
if (conv && m_untangled) break;
//if (iter == 5) break;
//if (iter == 0) exit(1);
}
eMesh->save_as("outer_iter_"+toString(outer)+"_"+toString(stage)+"_mesh.e");
}
eMesh->copy_field(coord_field_lagged, coord_field);
}
//if (!get_parallel_rank())
MPI_Barrier( MPI_COMM_WORLD );
std::cout << "\nP[" << get_parallel_rank() << "] tmp srk PMMParallelReferenceMeshSmoother: running shape improver... done \n" << std::endl;
MSQ_ERRRTN(err);
}
void compute_elem_mesh_size_ratio(
PerceptMesh& eMesh,
ScalarFieldType* elem_ratio_field,
const double &global_error_tol)
{
const int spatial_dim = eMesh.get_spatial_dim();
double local_error_tol = global_error_tol;
static bool first_run = true;
stk::mesh::Part * activeElementsPart = eMesh.get_non_const_part("refine_active_elements_part");
stk::mesh::Selector selector = first_run ?
eMesh.get_fem_meta_data()->locally_owned_part() :
( eMesh.get_fem_meta_data()->locally_owned_part() & (*activeElementsPart) );
first_run = false;
std::vector<unsigned> count ;
stk::mesh::count_entities( selector, *eMesh.get_bulk_data(), count );
const double num_elems = (double) count[eMesh.element_rank()];
local_error_tol /= sqrt(num_elems);
std::vector<stk::mesh::Bucket*> buckets;
stk::mesh::get_buckets( selector, eMesh.get_bulk_data()->buckets( eMesh.element_rank() ), buckets );
for ( vector<stk::mesh::Bucket*>::const_iterator k = buckets.begin() ; k != buckets.end() ; ++k ) {
stk::mesh::Bucket & bucket = **k ;
shards::CellTopology ct = stk::mesh::fem::get_cell_topology(bucket);
const int Nnpe = ct.getNodeCount();
std::vector<double> nodal_interp(Nnpe);
std::vector<double> nodal_coords(Nnpe*spatial_dim);
const unsigned num_elems_in_bucket = bucket.size();
for (unsigned i = 0; i < num_elems_in_bucket; i++) {
stk::mesh::Entity& element = bucket[i];
// gather nodal coords and compute centroid
std::vector<double> centroid(spatial_dim, 0.0);
stk::mesh::PairIterRelation elem_nodes = element.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
for (unsigned inode=0; inode < elem_nodes.size(); inode++) {
stk::mesh::Entity *node = elem_nodes[inode].entity();
double *coords = stk::mesh::field_data( *eMesh.get_coordinates_field() , *node);
for (int d=0; d<spatial_dim; d++) {
centroid[d] += coords[d];
nodal_coords[inode*spatial_dim+d] = coords[d];
}
exact_nodal_solution(coords, &nodal_interp[inode], spatial_dim);
}
for (int d=0; d<spatial_dim; d++) {
centroid[d] /= (double) Nnpe;
}
// calc interpolation error at midpoint
double eval_centroid;
exact_nodal_solution(¢roid[0], &eval_centroid, spatial_dim);
double interp_centroid = 0.0;
for (unsigned inode=0; inode < elem_nodes.size(); inode++) {
interp_centroid += nodal_interp[inode];
}
interp_centroid /= (double) Nnpe;
const double err_centroid = eval_centroid - interp_centroid;
// HACK triangles for now
const double area = triangle_area(nodal_coords);
const double local_error = fabs(err_centroid) * area;
double *ratio = stk::mesh::field_data( *elem_ratio_field , element);
// calc elem ratio
*ratio = sqrt(local_error / local_error_tol);
}
}
}