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);
}
double PMMParallelReferenceMeshSmoother2::run_one_iteration( Mesh* mesh, MeshDomain *domain,
MsqError& err )
{
PerceptMesquiteMesh *pmm = dynamic_cast<PerceptMesquiteMesh *>(mesh);
PerceptMesh *eMesh = pmm->getPerceptMesh();
int spatialDim = m_eMesh->get_spatial_dim();
stk_classic::mesh::FieldBase *cg_g_field = eMesh->get_field("cg_g");
stk_classic::mesh::FieldBase *cg_r_field = eMesh->get_field("cg_r");
stk_classic::mesh::FieldBase *cg_d_field = eMesh->get_field("cg_d");
stk_classic::mesh::FieldBase *cg_s_field = eMesh->get_field("cg_s");
stk_classic::mesh::Selector on_locally_owned_part = ( eMesh->get_fem_meta_data()->locally_owned_part() );
stk_classic::mesh::Selector on_globally_shared_part = ( eMesh->get_fem_meta_data()->globally_shared_part() );
bool total_valid=true;
bool reduced_metric=false;
m_dmax = 0.0;
get_gradient(mesh, domain);
{
/// r = -g
eMesh->nodal_field_axpby(-1.0, cg_g_field, 0.0, cg_r_field);
/// s = r (allows for preconditioning later s = M^-1 r)
eMesh->copy_field(cg_s_field, cg_r_field);
/// d = s
eMesh->copy_field(cg_d_field, cg_s_field);
/// dnew = r.d
m_dnew = eMesh->nodal_field_dot(cg_r_field, cg_d_field);
}
double metric_orig = total_metric(mesh, 0.0, 1.0, total_valid);
m_total_metric = metric_orig;
if (check_convergence() || metric_orig == 0.0)
{
PRINT_1( "tmp srk already converged m_dnew= " << m_dnew << " gradNorm= " << gradNorm << " m_d0= " << m_d0 );
//update_node_positions
return total_metric(mesh,0.0,1.0, total_valid);
}
// node loop: local line search
double alpha_min = 1.e+30;
double alpha_max = 0.0;
{
const std::vector<stk_classic::mesh::Bucket*> & buckets = eMesh->get_bulk_data()->buckets( eMesh->node_rank() );
for ( std::vector<stk_classic::mesh::Bucket*>::const_iterator k = buckets.begin() ; k != buckets.end() ; ++k )
{
// update local and globally shared
//if (on_locally_owned_part(**k) || on_globally_shared_part(**k))
if (on_locally_owned_part(**k))
{
stk_classic::mesh::Bucket & bucket = **k ;
const unsigned num_nodes_in_bucket = bucket.size();
for (unsigned i_node = 0; i_node < num_nodes_in_bucket; i_node++)
{
stk_classic::mesh::Entity& node = bucket[i_node];
bool fixed = pmm->get_fixed_flag(&node);
bool isGhostNode = !(on_locally_owned_part(node) || on_globally_shared_part(node));
if (fixed || isGhostNode)
{
continue;
}
//double edge_length_ave = m_eMesh->edge_length_ave(element);
double edge_length_ave = nodal_edge_length_ave(node);
double *coord_current = PerceptMesh::field_data(m_coord_field_current, node);
double *cg_d = PerceptMesh::field_data(cg_d_field, node);
double *cg_g = PerceptMesh::field_data(cg_g_field, node);
double local_scale = 0.0;
for (int i=0; i < spatialDim; i++)
{
local_scale = std::max(local_scale, std::abs(cg_g[i])/edge_length_ave);
}
local_scale = (local_scale < 1.0) ? 1.0 : 1.0/local_scale;
//PRINT("tmp srk node= " << node.identifier() << " iter= " << m_iter << " local_scale= " << local_scale);
/// line search
//get_nodal_gradient(node, cg_g_local);
double norm_gradient2 = 0.0;
for (int i=0; i < spatialDim; i++)
{
norm_gradient2 += cg_g[i]*cg_g[i];
}
double alpha = local_scale; // m_scale
if (std::sqrt(norm_gradient2) > edge_length_ave*1.e-8)
{
bool local_valid=true, local_valid_0=true, local_valid_1=true;
double metric_0 = nodal_metric(node, 0.0, coord_current, cg_d, local_valid_0);
double metric=0.0;
//double sigma=0.95;
double tau = 0.5;
double c0 = 1.e-4;
double armijo_offset_factor = c0*norm_gradient2;
bool converged = false;
while (!converged)
{
metric = nodal_metric(node, alpha, coord_current, cg_d, local_valid);
//converged = (metric > sigma*metric_0) && (alpha > 1.e-16);
double mfac = alpha*armijo_offset_factor;
converged = metric == 0.0 || (metric < metric_0 + mfac);
if (m_untangled) converged = converged && local_valid;
PRINT( "tmp srk node= " << node.identifier() << " iter= " << m_iter
<< " alpha= " << alpha << " metric_0= " << metric_0 << " metric= " << metric << " diff= " << metric - (metric_0 + mfac)
<< " m_untangled = " << m_untangled << " norm_gradient2= " << norm_gradient2
<< " local_valid= " << local_valid );
if (!converged)
alpha *= tau;
if (alpha < std::max(1.e-6*m_scale, 1.e-16))
{
PRINT_1( "tmp srk not conv node= " << node.identifier() << " iter= " << m_iter
<< " alpha= " << alpha << " metric_0= " << metric_0 << " metric= " << metric << " diff= " << metric - (metric_0 + mfac)
<< " m_untangled = " << m_untangled << " norm_gradient2= " << norm_gradient2
<< " local_valid= " << local_valid );
break;
}
}
//if (metric > sigma*metric_0)
if (!converged)
{
metric_0 = nodal_metric(node, 0.0, coord_current, cg_d, local_valid_0);
double metric_1 = nodal_metric(node, 1.e-6, coord_current, cg_d, local_valid_1);
PRINT_1( "tmp srk can't reduce metric, node= " << node.identifier() << " iter= " << m_iter
<< " alpha= " << alpha << " metric_0= " << metric_0 << " metric[1.e-6]= " << metric_1 << " diff[want neg]= " << metric_1 - metric_0
<< "\n m_untangled = " << m_untangled << " norm_gradient2= " << norm_gradient2
<< " local_valid= " << local_valid
<< " local_valid_0= " << local_valid_0
<< " local_valid_1= " << local_valid_1
<< " cg_d= " << cg_d[0] << " " << cg_d[1] << " edge_length_ave= " << edge_length_ave);
alpha = 0.0;
}
else
{
reduced_metric = true;
double a1 = alpha/2.;
double a2 = alpha;
double f0 = metric_0,
f1 = nodal_metric(node, a1, coord_current, cg_d, total_valid),
f2 = nodal_metric(node, a2, coord_current, cg_d, total_valid);
double den = 2.*(a2*(-f0 + f1) + a1*(f0 - f2));
double num = a2*a2*(f1-f0)+a1*a1*(f0-f2);
if (std::fabs(den) > 1.e-10)
{
double alpha_quadratic = num/den;
if (alpha_quadratic < 2.0*alpha)
{
double fm = nodal_metric(node, alpha_quadratic, coord_current, cg_d, total_valid);
//if (fm < f2 && (!m_untangled || total_valid))
if (fm < f2)
{
alpha = alpha_quadratic;
PRINT( "tmp srk alpha_quadratic= " << alpha_quadratic << " alpha= " << a2 );
}
}
}
}
}
alpha_min = std::min(alpha_min, alpha);
alpha_max = std::max(alpha_max, alpha);
// scale cg_d by local alpha
for (int i=0; i < spatialDim; i++)
{
cg_d[i] *= alpha;
}
} // node in bucket loop
}
} // bucket loop
}
/// check for valid mesh
double alpha_global = 1.0;
if (m_stage == 1)
{
bool converged = false;
while (!converged)
{
int num_invalid=0;
double metric_new = total_metric(mesh, alpha_global, 1.0, total_valid, &num_invalid);
PRINT_1( "tmp srk global alpha = " << alpha_global << " metric_new= " << metric_new << " total_valid= " << total_valid << " num_invalid= " << num_invalid);
if (total_valid)
{
converged = true;
break;
}
else
{
alpha_global *= 0.5;
}
if (alpha_global < 1.e-10)
{
break;
}
}
//if (metric > sigma*metric_0)
if (!converged)
{
bool local_valid_0=true, local_valid_1=true;
double metric_0 = total_metric(mesh,0.0, 1.0, local_valid_0);
double metric_1 = total_metric(mesh, 1.e-6, 1.0, local_valid_1);
PRINT_1( "tmp srk can't get valid mesh... "
" metric_0= " << metric_0 << " metric[1.e-6]= " << metric_1 << " diff[want neg]= " << metric_1 - metric_0
<< "\n m_untangled = " << m_untangled
<< " local_valid_0= " << local_valid_0
<< " local_valid_1= " << local_valid_1 );
}
}
/// x = x + alpha*d
m_dmax=0.0;
update_node_positions(mesh, alpha_global);
double metric_new = total_metric(mesh,0.0, 1.0, total_valid);
PRINT_1( "tmp srk iter= "<< m_iter << " dmax= " << m_dmax << " alpha_min= " << alpha_min << " alpha_max= " << alpha_max << " total_valid= " << total_valid);
if (m_stage == 1 && !total_valid)
{
throw std::runtime_error("created bad mesh");
}
//if (!reduced_metric || metric_new >= metric_orig)
if (!reduced_metric )
{
PRINT_1( "can't reduce metric, metric_new= " << metric_new << " metric_0 = " << metric_orig << " reduced_metric= " << reduced_metric);
throw std::runtime_error("can't reduce metric");
}
return metric_new;
}
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);
}
}
}