//----------------------------------------------------------------------------
//
// Random fracture criterion function.
//
bool
RandomCriterion::computeFractureCriterion(stk::mesh::Entity& entity, double p) {
// Fracture only defined on the boundary of the elements
stk::mesh::EntityRank rank = entity.entity_rank();
assert(rank == num_dim_ - 1);
stk::mesh::PairIterRelation neighbor_elems =
entity.relations(element_rank_);
// Need an element on each side
if(neighbor_elems.size() != 2)
return false;
bool is_open = false;
// All we need to do is generate a number between 0 and 1
double random = 0.5 + 0.5 * Teuchos::ScalarTraits<double>::random();
if(random < p) {
is_open = true;
}
return is_open;
}
bool
AAdapt::STKUnifUnrefineField::operator()(const stk::mesh::Entity element,
stk::mesh::FieldBase* field, const stk::mesh::BulkData& bulkData) {
const stk::mesh::PairIterRelation elem_nodes = element.relations(stk::topology::NODE_RANK);
unsigned num_node = elem_nodes.size();
double* f_data = stk::percept::PerceptMesh::field_data_entity(field, element);
Albany::AbstractSTKFieldContainer::VectorFieldType* coordField = m_eMesh.get_coordinates_field();
bool found = true;
for(unsigned inode = 0; inode < num_node; inode++) {
stk::mesh::Entity node = * elem_nodes[ inode ].entity();
double* coord_data = stk::percept::PerceptMesh::field_data(coordField, node);
if(coord_data[0] < 0.0 || coord_data[1] < 0.0) { // || coord_data[2] > 1.1)
found = false;
break;
}
}
if(found)
f_data[0] = -1.0;
else
f_data[0] = 0.0;
return false; // don't terminate the loop
}
void SideConnector::connect_side_to_all_elements(stk::mesh::Entity sideEntity, stk::mesh::Entity elemEntity, int elemSide)
{
connect_side_to_elem(sideEntity, elemEntity, elemSide);
stk::mesh::impl::LocalId elemLocalId = m_entity_to_local_id[elemEntity.local_offset()];
connect_side_to_coincident_elements(sideEntity, elemLocalId, elemSide);
connect_side_to_adjacent_elements(sideEntity, elemLocalId, elemSide);
}
int IEdgeAdapter::markUnrefine(const stk::mesh::Entity& element)
{
const CellTopologyData * const cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(element);
CellTopology cell_topo(cell_topo_data);
const mesh::PairIterRelation elem_nodes = element.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
VectorFieldType* coordField = m_eMesh.get_coordinates_field();
unsigned numSubDimNeededEntities = 0;
numSubDimNeededEntities = cell_topo_data->edge_count;
bool unrefAllEdges = true;
for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++)
{
stk::mesh::Entity & node0 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[0]].entity();
stk::mesh::Entity & node1 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[1]].entity();
double * const coord0 = stk::mesh::field_data( *coordField , node0 );
double * const coord1 = stk::mesh::field_data( *coordField , node1 );
int markInfo = mark(element, iSubDimOrd, node0, node1, coord0, coord1, 0);
bool do_unref = markInfo & DO_UNREFINE;
if (!do_unref)
{
unrefAllEdges = false;
break;
}
}
if (unrefAllEdges)
return -1;
else
return 0;
}
bool gather_field_data(unsigned expected_num_rel, const field_type & field,
const stk::mesh::Entity & entity,
typename stk::mesh::FieldTraits<field_type>::data_type * dst,
stk::mesh::EntityRank entity_rank, const int dim)
{
typedef typename stk::mesh::FieldTraits<field_type>::data_type T;
stk::mesh::PairIterRelation rel = entity.relations(entity_rank);
bool result = expected_num_rel == (unsigned) rel.size();
if (result)
{
// Iterate over field data for each related entity and copy data
// into src for one entity at a time
T * const dst_end = dst + dim * expected_num_rel;
for (; dst < dst_end; ++rel, dst += dim)
{
const T* src = field_data(field, *rel->entity());
if (!src)
{
break;
}
// FIXME:
if (dim == 1) stk::Copy<1>(dst, src);
if (dim == 2) stk::Copy<2>(dst, src);
if (dim == 3) stk::Copy<3>(dst, src);
}
result = dst == dst_end;
}
return result;
}
bool
AAdapt::STKUnifRefineField::operator()(const stk::mesh::Entity element,
stk::mesh::FieldBase* field, const stk::mesh::BulkData& bulkData) {
/*
double plane_point[3] = {2, 0, 0};
double plane_normal[3] = {1, .5, -.5};
*/
double plane_point[3] = {0, 0.7, 0};
double plane_normal[3] = {0, 1, 0};
const stk::mesh::PairIterRelation elem_nodes = element.relations(stk::topology::NODE_RANK);
unsigned num_node = elem_nodes.size();
double* f_data = stk::percept::PerceptMesh::field_data_entity(field, element);
Albany::AbstractSTKFieldContainer::VectorFieldType* coordField =
m_eMesh.get_coordinates_field();
bool found = false;
for(unsigned inode = 0; inode < num_node - 1; inode++) {
stk::mesh::Entity node_i = * elem_nodes[ inode ].entity();
double* coord_data_i = stk::percept::PerceptMesh::field_data(coordField, node_i);
for(unsigned jnode = inode + 1; jnode < num_node; jnode++) {
stk::mesh::Entity node_j = * elem_nodes[ jnode ].entity();
double* coord_data_j = stk::percept::PerceptMesh::field_data(coordField, node_j);
double dot_0 = plane_dot_product(plane_point, plane_normal, coord_data_i);
double dot_1 = plane_dot_product(plane_point, plane_normal, coord_data_j);
// if edge crosses the plane...
if(dot_0 * dot_1 < 0) {
found = true;
break;
}
}
}
if(found) {
f_data[0] = 1.0;
// std::cout << "Splitting: " << element.identifier() << std::endl;
}
else {
f_data[0] = 0.0;
// std::cout << "Not splitting: " << element.identifier() << std::endl;
}
return false; // don't terminate the loop
}
KOKKOS_INLINE_FUNCTION unsigned get_bucket_id(stk::mesh::Entity entity) const
{
const stk::mesh::FastMeshIndex& meshIndex = constMeshIndices(entity.local_offset());
return meshIndex.bucket_id;
}
STK_FUNCTION unsigned get_index(stk::mesh::Entity entity) const
{
const stk::mesh::FastMeshIndex& meshIndex = constMeshIndices(entity.local_offset());
return meshIndex.bucket_id * bucketCapacity + meshIndex.bucket_ord;
}
bool helperSubDim(const stk::mesh::Entity& child_element, stk::mesh::FieldBase *field, const mesh::BulkData& bulkData)
{
EXCEPTWATCH;
const CellTopologyData * const child_cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(child_element);
CellTopology child_cell_topo(child_cell_topo_data);
int child_cell_dimension = child_cell_topo.getDimension();
int meta_dimension = mesh::fem::FEMMetaData::get_meta_data(mesh::fem::FEMMetaData::get(bulkData)).get_spatial_dimension();
// for now, only allow face (or edge)
VERIFY_OP_ON(child_cell_dimension, ==, meta_dimension - 1, "Dimensions don't match");
VectorFieldType& coord_field = *(mesh::fem::FEMMetaData::get(bulkData)).get_field<VectorFieldType>("coordinates");
// FIXME for fields not on a Node
unsigned nDOF = m_nDOFs;
unsigned nCells = PerceptMesh::size1(child_element);
m_count_elems += nCells;
typedef IntrepidManager IM;
unsigned cubDegree = m_cubDegree;
const stk::mesh::PairIterRelation parent_elements = child_element.relations(child_element.entity_rank() + 1);
VERIFY_OP_ON(parent_elements.size(), ==, 1, "cant find parent");
const stk::mesh::Entity& element = *parent_elements[0].entity();
unsigned i_face = parent_elements[0].identifier();
const CellTopologyData * const cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(element);
CellTopology cell_topo(cell_topo_data);
int cell_dimension = cell_topo.getDimension();
VERIFY_OP_ON(cell_dimension, ==, meta_dimension , "Dimensions don't match");
IM im(Elements_Tag(nCells), cell_topo, cubDegree);
IM imChild(Elements_Tag(nCells), child_cell_topo, cubDegree);
unsigned numCubPoints_child = imChild.m_cub->getNumPoints();
im.m_Cub_Points_Tag = Cub_Points_Tag(numCubPoints_child);
if (0)
{
std::cout << "numCubPoints_child= " << numCubPoints_child
<< " parent rank= " << element.entity_rank()
<< " parent topo= " << cell_topo.getName()
<< std::endl;
}
// FIXME
im.m_DOFs_Tag.num = m_nDOFs;
// FIXME
// _c suffix is for the child (face) element
IM::Jacobian J (im);
IM::FaceNormal fn (im);
//IM::JacobianDet dJ (im);
IM::CubaturePoints xi (im);
IM::CubaturePoints xi_c (imChild);
IM::CellWorkSet cn (im);
IM::CubatureWeights wt (im);
IM::CubatureWeights wt_c (imChild);
IM::PhysicalCoords pc (im);
IM::IntegrandValues iv (im);
IM::IntegrandValuesDOF ivD (im);
IM::Integral Io (im);
IM::Bases Nb (im);
IM::WeightedMeasure wXfn (im);
IM::FieldValues fv (im);
imChild.m_cub->getCubature(xi_c, wt_c);
unsigned spaceDim = im.m_Spatial_Dim_Tag.num;
PerceptMesh::fillCellNodes(element, &coord_field, cn, spaceDim);
// get parent cell integration points
// Map Gauss points on quad to reference face: paramGaussPoints -> refGaussPoints
CellTools<double>::mapToReferenceSubcell(xi,
xi_c,
2, i_face, cell_topo); // FIXME magic
// get jacobian
J(xi, cn, cell_topo);
//dJ(J);
//shards::ArrayVector<double, shards::NaturalOrder, Elements_Tag, Cub_Points_Tag > fn_Norm;
// FIXME
//fn(J, i_face, cell_topo);
MDArray J_mda;
J.copyTo(J_mda);
MDArray fn_mda(im.m_Elements_Tag.num, numCubPoints_child, spaceDim);
CellTools<double>::getPhysicalFaceNormals(fn_mda, J_mda, i_face, cell_topo);
/// get norm of fn
for (int icell = 0; icell < im.m_Elements_Tag.num; icell++)
{
for (int ipt = 0; ipt < (int)numCubPoints_child; ipt++)
{
double sum = 0.0;
for (int i = 0; i < (int)spaceDim; i++)
{
sum += square(fn_mda(icell, ipt, i));
}
wXfn(icell, ipt) = std::sqrt(sum) * wt_c(ipt);
}
}
if (0)
{
using namespace shards;
//std::cout << "dJ= \n" << dJ << std::endl;
std::cout << "wXfn= \n" << wXfn << std::endl;
std::cout << "xi= \n" << xi << std::endl;
std::cout << "wt= \n" << wt << std::endl;
std::cout << "cn= \n" << cn << std::endl;
Util::setDoPause(true);
Util::pause(true);
}
// get physical coordinates at integration points
pc(cn, xi);
// get bases
#if 1
// FIXME
MDArray xi_mda;
xi.copyTo(xi_mda);
Nb(element, xi_mda);
#else
Nb(element, xi);
#endif
// apply integrand (right now we have MDArray hard-coded... FIXME - templatize on its type)
// it should look like this (one instead of multiple lines):
#if 0
m_integrand(pc, v);
#else
MDArray pc_mda;
pc.copyTo(pc_mda);
std::vector<int> ivDims;
ivD.dimensions( ivDims);
/// NOTE: m_integrand requires the ranks of in/out MDArrays to be such that out_rank >= in_rank
/// Thus, we use IntegrandValuesDOF with [DOF] = 1, and then copy the result to IntegrandValues
/// which does not have the additional rightmost DOF index (Intrepid doesn't have the concept of
/// DOF's, it works on scalars only for the integration routines, or at least that's how I understand
/// it currently.
// create an array that stk::percept::Function will like to hold the results
ivDims[ivDims.size()-1] = m_nDOFs;
MDArray iv_mda ( Teuchos::Array<int>(ivDims.begin(), ivDims.end()));
if (m_turboOpt == TURBO_ELEMENT || m_turboOpt == TURBO_BUCKET)
{
m_integrand(pc_mda, iv_mda, element, xi_mda);
}
else
{
m_integrand(pc_mda, iv_mda);
}
// now, copy from the results to an array that Intrepid::integrate will like
#endif
for (unsigned iDof = 0; iDof < nDOF; iDof++)
{
iv.copyFrom(im, iv_mda, iDof);
// get the integral
if (m_accumulation_type == ACCUMULATE_SUM)
{
Io(iv, wXfn, COMP_BLAS);
}
//optional design:
//
// Io(integrand(pc_mda, v), wXdJ(w, dJ(J(xi, c, cell_topo)), COMP_BLAS);
for (unsigned iCell = 0; iCell < nCells; iCell++)
{
// if (Util::getFlag(0))
// {
// std::cout << "tmp Io(iCell)= " << Io(iCell) << std::endl;
// Util::pause(true, "Io(iCell)");
// }
if (m_accumulation_type == ACCUMULATE_SUM)
{
m_accumulation_buffer[iDof] += Io(iCell);
}
else if (m_accumulation_type == ACCUMULATE_MAX)
{
double valIo = 0.0;
for (int ivpts = 0; ivpts < iv.dimension(1); ivpts++)
{
valIo = std::max(valIo, iv((int)iCell, ivpts));
}
//std::cout << "m_accumulation_buffer[iDof] = " << m_accumulation_buffer[iDof] << " valIO= " << valIo << std::endl;
m_accumulation_buffer[iDof] = std::max(m_accumulation_buffer[iDof], valIo);
}
}
}
return false;
}
void TestLocalRefinerTri2::
refineMethodApply(NodeRegistry::ElementFunctionPrototype function, const stk::mesh::Entity& element, vector<NeededEntityType>& needed_entity_ranks)
{
const CellTopologyData * const cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(element);
CellTopology cell_topo(cell_topo_data);
const mesh::PairIterRelation elem_nodes = element.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
VectorFieldType* coordField = m_eMesh.get_coordinates_field();
for (unsigned ineed_ent=0; ineed_ent < needed_entity_ranks.size(); ineed_ent++)
{
unsigned numSubDimNeededEntities = 0;
stk::mesh::EntityRank needed_entity_rank = needed_entity_ranks[ineed_ent].first;
if (needed_entity_rank == m_eMesh.edge_rank())
{
numSubDimNeededEntities = cell_topo_data->edge_count;
}
else if (needed_entity_rank == m_eMesh.face_rank())
{
numSubDimNeededEntities = cell_topo_data->side_count;
}
else if (needed_entity_rank == m_eMesh.element_rank())
{
numSubDimNeededEntities = 1;
}
// see how many edges are already marked
int num_marked=0;
if (needed_entity_rank == m_eMesh.edge_rank())
{
for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++)
{
bool is_empty = m_nodeRegistry->is_empty( element, needed_entity_rank, iSubDimOrd);
if (!is_empty) ++num_marked;
}
}
for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++)
{
/// note: at this level of granularity we can do single edge refinement, hanging nodes, etc.
//SubDimCell_SDSEntityType subDimEntity;
//getSubDimEntity(subDimEntity, element, needed_entity_rank, iSubDimOrd);
//bool is_empty = m_nodeRegistry->is_empty( element, needed_entity_rank, iSubDimOrd);
//if(1||!is_empty)
if (needed_entity_rank == m_eMesh.edge_rank())
{
stk::mesh::Entity & node0 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[0]].entity();
stk::mesh::Entity & node1 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[1]].entity();
double * const coord0 = stk::mesh::field_data( *coordField , node0 );
double * const coord1 = stk::mesh::field_data( *coordField , node1 );
// only refine diagonals of the split quads
if (m_diagonals)
{
if ( std::abs(coord0[0]-coord1[0]) > 1.e-3 && std::abs(coord0[1]-coord1[1]) > 1.e-3 )
{
(m_nodeRegistry ->* function)(element, needed_entity_ranks[ineed_ent], iSubDimOrd, true);
}
}
else
{
if ( std::abs(coord0[0]-coord1[0]) < 1.e-3 && std::abs(coord0[1]-coord1[1]) > 1.e-3 )
{
(m_nodeRegistry ->* function)(element, needed_entity_ranks[ineed_ent], iSubDimOrd, true);
}
}
}
} // iSubDimOrd
} // ineed_ent
}
inline int Albany::STKDiscretization::gid(const stk::mesh::Entity& node) const
{ return node.identifier()-1; }
unsigned
Albany::STKDiscretization::determine_local_side_id( const stk::mesh::Entity & elem , stk::mesh::Entity & side ) {
using namespace stk;
const CellTopologyData * const elem_top = mesh::fem::get_cell_topology( elem ).getCellTopologyData();
const mesh::PairIterRelation elem_nodes = elem.relations( mesh::fem::FEMMetaData::NODE_RANK );
const mesh::PairIterRelation side_nodes = side.relations( mesh::fem::FEMMetaData::NODE_RANK );
int side_id = -1 ;
if(elem_nodes.size() == 0 || side_nodes.size() == 0){ // Node relations are not present, look at elem->face
int elem_rank = elem.entity_rank();
const mesh::PairIterRelation elem_sides = elem.relations( elem_rank - 1);
for ( unsigned i = 0 ; i < elem_sides.size() ; ++i ) {
const stk::mesh::Entity & elem_side = *elem_sides[i].entity();
if(elem_side.identifier() == side.identifier()){ // Found the local side in the element
side_id = static_cast<int>(i);
return side_id;
}
}
if ( side_id < 0 ) {
std::ostringstream msg ;
msg << "determine_local_side_id( " ;
msg << elem_top->name ;
msg << " , Element[ " ;
msg << elem.identifier();
msg << " ]{" ;
for ( unsigned i = 0 ; i < elem_sides.size() ; ++i ) {
msg << " " << elem_sides[i].entity()->identifier();
}
msg << " } , Side[ " ;
msg << side.identifier();
msg << " ] ) FAILED" ;
throw std::runtime_error( msg.str() );
}
}
else { // Conventional elem->node - side->node connectivity present
for ( unsigned i = 0 ; side_id == -1 && i < elem_top->side_count ; ++i ) {
const CellTopologyData & side_top = * elem_top->side[i].topology ;
const unsigned * side_map = elem_top->side[i].node ;
if ( side_nodes.size() == side_top.node_count ) {
side_id = i ;
for ( unsigned j = 0 ;
side_id == static_cast<int>(i) && j < side_top.node_count ; ++j ) {
mesh::Entity * const elem_node = elem_nodes[ side_map[j] ].entity();
bool found = false ;
for ( unsigned k = 0 ; ! found && k < side_top.node_count ; ++k ) {
found = elem_node == side_nodes[k].entity();
}
if ( ! found ) { side_id = -1 ; }
}
}
}
if ( side_id < 0 ) {
std::ostringstream msg ;
msg << "determine_local_side_id( " ;
msg << elem_top->name ;
msg << " , Element[ " ;
msg << elem.identifier();
msg << " ]{" ;
for ( unsigned i = 0 ; i < elem_nodes.size() ; ++i ) {
msg << " " << elem_nodes[i].entity()->identifier();
}
msg << " } , Side[ " ;
msg << side.identifier();
msg << " ]{" ;
for ( unsigned i = 0 ; i < side_nodes.size() ; ++i ) {
msg << " " << side_nodes[i].entity()->identifier();
}
msg << " } ) FAILED" ;
throw std::runtime_error( msg.str() );
}
}
return static_cast<unsigned>(side_id) ;
}
void TestLocalRefinerTet_N_2_1::
refineMethodApply(NodeRegistry::ElementFunctionPrototype function, const stk::mesh::Entity& element, vector<NeededEntityType>& needed_entity_ranks)
{
//static int n_seq = 400;
const CellTopologyData * const cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(element);
CellTopology cell_topo(cell_topo_data);
const mesh::PairIterRelation elem_nodes = element.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
//VectorFieldType* coordField = m_eMesh.get_coordinates_field();
for (unsigned ineed_ent=0; ineed_ent < needed_entity_ranks.size(); ineed_ent++)
{
unsigned numSubDimNeededEntities = 0;
stk::mesh::EntityRank needed_entity_rank = needed_entity_ranks[ineed_ent].first;
if (needed_entity_rank == m_eMesh.edge_rank())
{
numSubDimNeededEntities = cell_topo_data->edge_count;
}
else if (needed_entity_rank == m_eMesh.face_rank())
{
numSubDimNeededEntities = cell_topo_data->side_count;
}
else if (needed_entity_rank == m_eMesh.element_rank())
{
numSubDimNeededEntities = 1;
}
// see how many edges are already marked
int num_marked=0;
if (needed_entity_rank == m_eMesh.edge_rank())
{
for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++)
{
bool is_empty = m_nodeRegistry->is_empty( element, needed_entity_rank, iSubDimOrd);
if (!is_empty) ++num_marked;
}
}
for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++)
{
/// note: at this level of granularity we can do single edge refinement, hanging nodes, etc.
//SubDimCell_SDSEntityType subDimEntity;
//getSubDimEntity(subDimEntity, element, needed_entity_rank, iSubDimOrd);
//bool is_empty = m_nodeRegistry->is_empty( element, needed_entity_rank, iSubDimOrd);
//if(1||!is_empty)
if (needed_entity_rank == m_eMesh.edge_rank())
{
#if 0
stk::mesh::Entity & node0 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[0]].entity();
stk::mesh::Entity & node1 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[1]].entity();
double * const coord0 = stk::mesh::field_data( *coordField , node0 );
double * const coord1 = stk::mesh::field_data( *coordField , node1 );
// vertical line position
const double vx = 0.21;
// horizontal line position
const double vy = 1.21;
// choose to refine or not
if (
( std::fabs(coord0[0]-coord1[0]) > 1.e-3 &&
( (coord0[0] < vx && vx < coord1[0]) || (coord1[0] < vx && vx < coord0[0]) )
)
||
( std::fabs(coord0[1]-coord1[1]) > 1.e-3 &&
( (coord0[1] < vy && vy < coord1[1]) || (coord1[1] < vy && vy < coord0[1]) )
)
)
{
(m_nodeRegistry ->* function)(element, needed_entity_ranks[ineed_ent], iSubDimOrd, true);
}
#endif
// mark first m_edge_mark_bitcode edges
std::cout << "tmp TestLocalRefinerTet_N_2_1 element.identifier() = " << element.identifier()
<< " m_edge_mark_bitcode= " << m_edge_mark_bitcode << std::endl;
if ( ((1 << iSubDimOrd) & m_edge_mark_bitcode) && element.identifier() == 1)
(m_nodeRegistry ->* function)(element, needed_entity_ranks[ineed_ent], iSubDimOrd, true);
}
} // iSubDimOrd
} // ineed_ent
}
void
createNewElements(percept::PerceptMesh& eMesh, NodeRegistry& nodeRegistry,
stk::mesh::Entity& element, NewSubEntityNodesType& new_sub_entity_nodes, vector<stk::mesh::Entity *>::iterator& element_pool,
stk::mesh::FieldBase *proc_rank_field=0)
{
const CellTopologyData * const cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(element);
typedef boost::tuple<stk::mesh::EntityId, stk::mesh::EntityId, stk::mesh::EntityId, stk::mesh::EntityId> quad_tuple_type;
static vector<quad_tuple_type> elems(4);
CellTopology cell_topo(cell_topo_data);
const stk::mesh::PairIterRelation elem_nodes = element.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
//stk::mesh::Part & active = mesh->ActivePart();
//stk::mesh::Part & quad4 = mesh->QuadPart();
std::vector<stk::mesh::Part*> add_parts;
std::vector<stk::mesh::Part*> remove_parts;
//add_parts.push_back( &active );
//FIXME
//add_parts.push_back( const_cast<mesh::Part*>( eMesh.getPart(m_toTopoPartName) ));
add_parts = m_toParts;
double tmp_x[3];
for (int iedge = 0; iedge < 4; iedge++)
{
double * mp = midPoint(EDGE_COORD(iedge,0), EDGE_COORD(iedge,1), eMesh.get_spatial_dim(), tmp_x);
if (!EDGE_N(iedge))
{
std::cout << "P[" << eMesh.get_rank() << " nid ## = 0 << " << std::endl;
}
eMesh.createOrGetNode(EDGE_N(iedge), mp);
}
nodeRegistry.makeCentroidCoords(*const_cast<stk::mesh::Entity *>(&element), m_eMesh.element_rank(), 0u);
// new_sub_entity_nodes[i][j]
#define CENTROID_N NN(m_primaryEntityRank,0)
elems[0] = quad_tuple_type(VERT_N(0), EDGE_N(0), CENTROID_N, EDGE_N(3));
elems[1] = quad_tuple_type(VERT_N(1), EDGE_N(1), CENTROID_N, EDGE_N(0));
elems[2] = quad_tuple_type(VERT_N(2), EDGE_N(2), CENTROID_N, EDGE_N(1));
elems[3] = quad_tuple_type(VERT_N(3), EDGE_N(3), CENTROID_N, EDGE_N(2));
#undef CENTROID_N
// write a diagram of the refinement pattern as a vtk file, or a latex/tikz/pgf file
#define WRITE_DIAGRAM 0
#if WRITE_DIAGRAM
#endif
for (unsigned ielem=0; ielem < elems.size(); ielem++)
{
stk::mesh::Entity& newElement = *(*element_pool);
if (proc_rank_field)
{
double *fdata = stk::mesh::field_data( *static_cast<const ScalarFieldType *>(proc_rank_field) , newElement );
//fdata[0] = double(m_eMesh.get_rank());
fdata[0] = double(newElement.owner_rank());
}
eMesh.get_bulk_data()->change_entity_parts( newElement, add_parts, remove_parts );
{
if (!elems[ielem].get<0>())
{
std::cout << "P[" << eMesh.get_rank() << " nid = 0 << " << std::endl;
exit(1);
}
}
eMesh.get_bulk_data()->declare_relation(newElement, eMesh.createOrGetNode(elems[ielem].get<0>()), 0);
eMesh.get_bulk_data()->declare_relation(newElement, eMesh.createOrGetNode(elems[ielem].get<1>()), 1);
eMesh.get_bulk_data()->declare_relation(newElement, eMesh.createOrGetNode(elems[ielem].get<2>()), 2);
eMesh.get_bulk_data()->declare_relation(newElement, eMesh.createOrGetNode(elems[ielem].get<3>()), 3);
set_parent_child_relations(eMesh, element, newElement, ielem);
element_pool++;
}
}
//----------------------------------------------------------------------------
//
// Stress fracture criterion function.
//
bool
StressFracture::computeFractureCriterion(stk::mesh::Entity entity, double p) {
// Fracture only defined on the boundary of the elements
stk::mesh::EntityRank rank = entity.entity_rank();
assert(rank == num_dim_ - 1);
stk::mesh::PairIterRelation neighbor_elems =
entity.relations(element_rank_);
// Need an element on each side of the edge
if(neighbor_elems.size() != 2)
return false;
// Note that these are element GIDs
stk::mesh::EntityId elem_0_Id =
neighbor_elems[0].entity()->identifier();
stk::mesh::EntityId elem_1_Id =
neighbor_elems[1].entity()->identifier();
Albany::WsLIDList& elemGIDws = stk_.getElemGIDws();
// Have two elements, one on each size of the edge (or
// face). Check and see if the stresses are such that we want to
// split the mesh here.
//
// Initial hack - GAH: if the average stress between two elements
// is above the input value "Fracture Stress", split them at the
// edge
bool is_open = false;
// Check criterion
// If average between cells is above crit, split
// if (0.5 * (avg_stresses[elemGIDws[elem_0_Id].ws][elemGIDws[elem_0_Id].LID] +
// avg_stresses[elemGIDws[elem_1_Id].ws][elemGIDws[elem_1_Id].LID]) >= crit_stress){
// If stress difference across face it above crit, split
// if (fabs(avg_stresses[elemGIDws[elem_0_Id].ws][elemGIDws[elem_0_Id].LID] -
// avg_stresses[elemGIDws[elem_1_Id].ws][elemGIDws[elem_1_Id].LID]) >= crit_stress){
// Just split the doggone elements already!!!
if(p == 5) {
if((elem_0_Id - 1 == 35 && elem_1_Id - 1 == 140) ||
(elem_1_Id - 1 == 35 && elem_0_Id - 1 == 140)) {
is_open = true;
std::cout << "Splitting elements " << elem_0_Id - 1 << " and " << elem_1_Id - 1 << std::endl;
//std::cout << avg_stresses[elemGIDws[elem_0_Id].ws][elemGIDws[elem_0_Id].LID] << " " <<
// avg_stresses[elemGIDws[elem_1_Id].ws][elemGIDws[elem_1_Id].LID] << std::endl;
}
}
else if(p == 10) {
if((elem_0_Id - 1 == 42 && elem_1_Id - 1 == 147) ||
(elem_1_Id - 1 == 42 && elem_0_Id - 1 == 147)) {
is_open = true;
std::cout << "Splitting elements " << elem_0_Id - 1 << " and " << elem_1_Id - 1 << std::endl;
}
}
else if(p == 15) {
if((elem_0_Id - 1 == 49 && elem_1_Id - 1 == 154) ||
(elem_1_Id - 1 == 49 && elem_0_Id - 1 == 154)) {
is_open = true;
std::cout << "Splitting elements " << elem_0_Id - 1 << " and " << elem_1_Id - 1 << std::endl;
}
}
return is_open;
}
void
createNewElements(percept::PerceptMesh& eMesh, NodeRegistry& nodeRegistry,
stk::mesh::Entity& element, NewSubEntityNodesType& new_sub_entity_nodes, vector<stk::mesh::Entity *>::iterator& element_pool,
stk::mesh::FieldBase *proc_rank_field=0)
{
const CellTopologyData * const cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(element);
typedef boost::tuple<stk::mesh::EntityId, stk::mesh::EntityId> line_tuple_type;
static vector<line_tuple_type> elems(2);
CellTopology cell_topo(cell_topo_data);
const stk::mesh::PairIterRelation elem_nodes = element.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
std::vector<stk::mesh::Part*> add_parts;
std::vector<stk::mesh::Part*> remove_parts;
add_parts = m_toParts;
unsigned num_nodes_on_edge = new_sub_entity_nodes[m_eMesh.edge_rank()][0].size();
if (!num_nodes_on_edge)
return;
double coord_x[3];
for (int iedge = 0; iedge < 1; iedge++)
{
//double * mp = midPoint(EDGE_COORD(iedge,0), EDGE_COORD(iedge,1), eMesh.get_spatial_dim(), coord_x);
//double * mp = midPoint(FACE_COORD(iedge,0), FACE_COORD(iedge,1), eMesh.get_spatial_dim(), coord_x);
double * mp = midPoint(VERT_COORD(0), VERT_COORD(1), eMesh.get_spatial_dim(), coord_x);
if (!EDGE_N(iedge))
{
std::cout << "P[" << eMesh.get_rank() << " nid ## = 0 " << std::endl;
}
eMesh.createOrGetNode(EDGE_N(iedge), mp);
}
// FIXME
nodeRegistry.makeCentroidCoords(*const_cast<stk::mesh::Entity *>(&element), m_primaryEntityRank, 0u);
nodeRegistry.addToExistingParts(*const_cast<stk::mesh::Entity *>(&element), m_primaryEntityRank, 0u);
nodeRegistry.interpolateFields(*const_cast<stk::mesh::Entity *>(&element), m_primaryEntityRank, 0u);
Elem::CellTopology elem_celltopo = Elem::getCellTopology< FromTopology >();
const Elem::RefinementTopology* ref_topo_p = Elem::getRefinementTopology(elem_celltopo);
const Elem::RefinementTopology& ref_topo = *ref_topo_p;
#ifndef NDEBUG
unsigned num_child = ref_topo.num_child();
VERIFY_OP(num_child, == , 2, "createNewElements num_child problem");
bool homogeneous_child = ref_topo.homogeneous_child();
VERIFY_OP(homogeneous_child, ==, true, "createNewElements homogeneous_child");
#endif
// new_sub_entity_nodes[i][j]
//const UInt * const * child_nodes() const {
//const UInt * child_node_0 = ref_topo.child_node(0);
typedef Elem::StdMeshObjTopologies::RefTopoX RefTopoX;
RefTopoX& l2 = Elem::StdMeshObjTopologies::RefinementTopologyExtra< FromTopology > ::refinement_topology;
#define CENTROID_N NN(m_primaryEntityRank,0)
for (unsigned iChild = 0; iChild < 2; iChild++)
{
unsigned EN[2];
for (unsigned jNode = 0; jNode < 2; jNode++)
{
unsigned childNodeIdx = ref_topo.child_node(iChild)[jNode];
#ifndef NDEBUG
unsigned childNodeIdxCheck = l2[childNodeIdx].ordinal_of_node;
VERIFY_OP(childNodeIdx, ==, childNodeIdxCheck, "childNodeIdxCheck");
#endif
unsigned inode=0;
if (l2[childNodeIdx].rank_of_subcell == 0)
inode = VERT_N(l2[childNodeIdx].ordinal_of_subcell);
else if (l2[childNodeIdx].rank_of_subcell == 1)
inode = EDGE_N(l2[childNodeIdx].ordinal_of_subcell);
// else if (l2[childNodeIdx].rank_of_subcell == 2)
// inode = CENTROID_N;
EN[jNode] = inode;
}
elems[iChild] = line_tuple_type(EN[0], EN[1]);
}
#undef CENTROID_N
for (unsigned ielem=0; ielem < elems.size(); ielem++)
{
stk::mesh::Entity& newElement = *(*element_pool);
#if 0
if (proc_rank_field && proc_rank_field->rank() == m_eMesh.edge_rank()) //&& m_eMesh.get_spatial_dim()==1)
{
double *fdata = stk::mesh::field_data( *static_cast<const ScalarFieldType *>(proc_rank_field) , newElement );
//fdata[0] = double(m_eMesh.get_rank());
fdata[0] = double(newElement.owner_rank());
}
#endif
stk::mesh::FieldBase * proc_rank_field_edge = m_eMesh.get_field("proc_rank_edge");
if (proc_rank_field_edge)
{
double *fdata = stk::mesh::field_data( *static_cast<const ScalarFieldType *>(proc_rank_field_edge) , newElement );
fdata[0] = double(newElement.owner_rank());
//fdata[0] = 1234.56;
if (0)
std::cout << "P[" << m_eMesh.get_rank() << "] tmp set proc_rank_field_edge to value = " << newElement.owner_rank()
<< " for side element = " << newElement.identifier()
<< std::endl;
}
//eMesh.get_bulk_data()->change_entity_parts( newElement, add_parts, remove_parts );
change_entity_parts(eMesh, element, newElement);
{
if (!elems[ielem].get<0>())
{
std::cout << "P[" << eMesh.get_rank() << " nid = 0 " << std::endl;
exit(1);
}
}
eMesh.get_bulk_data()->declare_relation(newElement, eMesh.createOrGetNode(elems[ielem].get<0>()), 0);
eMesh.get_bulk_data()->declare_relation(newElement, eMesh.createOrGetNode(elems[ielem].get<1>()), 1);
set_parent_child_relations(eMesh, element, newElement, ielem);
element_pool++;
}
}
void IEdgeAdapter::
refineMethodApply(NodeRegistry::ElementFunctionPrototype function, const stk::mesh::Entity& element,
vector<NeededEntityType>& needed_entity_ranks)
{
const CellTopologyData * const cell_topo_data = stk::percept::PerceptMesh::get_cell_topology(element);
CellTopology cell_topo(cell_topo_data);
const mesh::PairIterRelation elem_nodes = element.relations(stk::mesh::fem::FEMMetaData::NODE_RANK);
VectorFieldType* coordField = m_eMesh.get_coordinates_field();
for (unsigned ineed_ent=0; ineed_ent < needed_entity_ranks.size(); ineed_ent++)
{
unsigned numSubDimNeededEntities = 0;
stk::mesh::EntityRank needed_entity_rank = needed_entity_ranks[ineed_ent].first;
if (needed_entity_rank == m_eMesh.edge_rank())
{
numSubDimNeededEntities = cell_topo_data->edge_count;
}
else if (needed_entity_rank == m_eMesh.face_rank())
{
numSubDimNeededEntities = cell_topo_data->side_count;
throw std::runtime_error("IEdgeAdapter::apply can't use IEdgeAdapter for RefinerPatterns that require face nodes");
}
else if (needed_entity_rank == m_eMesh.element_rank())
{
numSubDimNeededEntities = 1;
throw std::runtime_error("IEdgeAdapter::apply can't use IEdgeAdapter for RefinerPatterns that require volume nodes");
}
// see how many edges are already marked
int num_marked=0;
std::vector<int> edge_marks(numSubDimNeededEntities,0);
if (needed_entity_rank == m_eMesh.edge_rank())
{
for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++)
{
bool is_empty = m_nodeRegistry->is_empty( element, needed_entity_rank, iSubDimOrd);
if (!is_empty)
{
edge_marks[iSubDimOrd] = 1;
++num_marked;
}
}
}
for (unsigned iSubDimOrd = 0; iSubDimOrd < numSubDimNeededEntities; iSubDimOrd++)
{
if (needed_entity_rank == m_eMesh.edge_rank())
{
stk::mesh::Entity & node0 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[0]].entity();
stk::mesh::Entity & node1 = *elem_nodes[cell_topo_data->edge[iSubDimOrd].node[1]].entity();
double * const coord0 = stk::mesh::field_data( *coordField , node0 );
double * const coord1 = stk::mesh::field_data( *coordField , node1 );
int markInfo = mark(element, iSubDimOrd, node0, node1, coord0, coord1, &edge_marks);
bool needNodes = (DO_REFINE & markInfo);
{
(m_nodeRegistry ->* function)(element, needed_entity_ranks[ineed_ent], iSubDimOrd, needNodes);
}
}
} // iSubDimOrd
} // ineed_ent
}
/// modeled after code from Mesquite::IdealWeightMeanRatio::evaluate()
bool JacobianUtil::operator()(double& m, PerceptMesh& eMesh, stk::mesh::Entity& element, stk::mesh::FieldBase *coord_field,
const CellTopologyData * topology_data )
{
MsqError err;
static MsqMatrix<3,3> J;
static Vector3D n; // Surface normal for 2D objects
// Prism and Hex element descriptions
static const int locs_prism[6][4] = {{0, 1, 2, 3}, {1, 2, 0, 4},
{2, 0, 1, 5}, {3, 5, 4, 0},
{4, 3, 5, 1}, {5, 4, 3, 2}};
static const int locs_hex[8][4] = {{0, 1, 3, 4}, {1, 2, 0, 5},
{2, 3, 1, 6}, {3, 0, 2, 7},
{4, 7, 5, 0}, {5, 4, 6, 1},
{6, 5, 7, 2}, {7, 6, 4, 3}};
int i=0;
static const Vector3D d_con(1.0, 1.0, 1.0);
bool metric_valid = false;
if (!topology_data) topology_data = stk::percept::PerceptMesh::get_cell_topology(element);
stk::mesh::PairIterRelation v_i = element.relations(eMesh.node_rank());
m_num_nodes = v_i.size();
//#define VERTEX_2D(vi) vector_2D( eMesh.field_data(coord_field, *vi.entity() ) )
//#define VERTEX_3D(vi) vector_3D( eMesh.field_data(coord_field, *vi.entity() ) )
#define VERTEX_2D(vi) vector_2D( stk::mesh::field_data( *static_cast<const VectorFieldType *>(coord_field) , *vi.entity() ) )
#define VERTEX_3D(vi) vector_3D( stk::mesh::field_data( *static_cast<const VectorFieldType *>(coord_field) , *vi.entity() ) )
switch(topology_data->key)
{
case shards::Triangle<3>::key:
n[0] = 0; n[1] = 0; n[2] = 1;
mCoords[0] = VERTEX_2D(v_i[0]);
mCoords[1] = VERTEX_2D(v_i[1]);
mCoords[2] = VERTEX_2D(v_i[2]);
metric_valid = jacobian_matrix_2D(m, J, mCoords, n, d_con);
for (i = 0; i < 4; i++) { m_detJ[i] = m; m_J[i] = J; }
break;
case shards::Quadrilateral<4>::key:
n[0] = 0; n[1] = 0; n[2] = 1;
for (i = 0; i < 4; ++i) {
mCoords[0] = VERTEX_2D(v_i[locs_hex[i][0]]);
mCoords[1] = VERTEX_2D(v_i[locs_hex[i][1]]);
mCoords[2] = VERTEX_2D(v_i[locs_hex[i][2]]);
metric_valid = jacobian_matrix_2D(m_detJ[i], m_J[i], mCoords, n, d_con);
}
m = average_metrics(m_detJ, 4, err); MSQ_ERRZERO(err);
break;
case shards::Tetrahedron<4>::key:
mCoords[0] = VERTEX_3D(v_i[0]);
mCoords[1] = VERTEX_3D(v_i[1]);
mCoords[2] = VERTEX_3D(v_i[2]);
mCoords[3] = VERTEX_3D(v_i[3]);
metric_valid = jacobian_matrix_3D(m, J, mCoords, n, d_con);
for (i = 0; i < 4; i++) { m_detJ[i] = m; m_J[i] = J; }
break;
case shards::Pyramid<5>::key:
for (i = 0; i < 4; ++i) {
mCoords[0] = VERTEX_3D(v_i[ i ]);
mCoords[1] = VERTEX_3D(v_i[(i+1)%4]);
mCoords[2] = VERTEX_3D(v_i[(i+3)%4]);
mCoords[3] = VERTEX_3D(v_i[ 4 ]);
metric_valid = jacobian_matrix_3D(m_detJ[i], m_J[i], mCoords, n, d_con);
}
// FIXME
m_J[4] = (m_J[0]+m_J[1]+m_J[2]+m_J[3]);
m_J[4] *= 0.25;
m_detJ[4] = det(m_J[4]);
m = average_metrics(m_detJ, 5, err); MSQ_ERRZERO(err);
break;
case shards::Wedge<6>::key:
for (i = 0; i < 6; ++i) {
mCoords[0] = VERTEX_3D(v_i[locs_prism[i][0]]);
mCoords[1] = VERTEX_3D(v_i[locs_prism[i][1]]);
mCoords[2] = VERTEX_3D(v_i[locs_prism[i][2]]);
mCoords[3] = VERTEX_3D(v_i[locs_prism[i][3]]);
metric_valid = jacobian_matrix_3D(m_detJ[i], m_J[i], mCoords, n, d_con);
}
m = average_metrics(m_detJ, 6, err); MSQ_ERRZERO(err);
break;
case shards::Hexahedron<8>::key:
for (i = 0; i < 8; ++i) {
mCoords[0] = VERTEX_3D(v_i[locs_hex[i][0]]);
mCoords[1] = VERTEX_3D(v_i[locs_hex[i][1]]);
mCoords[2] = VERTEX_3D(v_i[locs_hex[i][2]]);
mCoords[3] = VERTEX_3D(v_i[locs_hex[i][3]]);
metric_valid = jacobian_matrix_3D(m_detJ[i], m_J[i], mCoords, n, d_con);
}
m = average_metrics(m_detJ, 8, err); MSQ_ERRZERO(err);
break;
// unimplemented
case shards::Node::key:
case shards::Particle::key:
case shards::Line<2>::key:
case shards::Line<3>::key:
case shards::ShellLine<2>::key:
case shards::ShellLine<3>::key:
case shards::Beam<2>::key:
case shards::Beam<3>::key:
case shards::Triangle<4>::key:
case shards::Triangle<6>::key:
case shards::ShellTriangle<3>::key:
case shards::ShellTriangle<6>::key:
case shards::Quadrilateral<8>::key:
case shards::Quadrilateral<9>::key:
case shards::ShellQuadrilateral<4>::key:
case shards::ShellQuadrilateral<8>::key:
case shards::ShellQuadrilateral<9>::key:
case shards::Tetrahedron<8>::key:
case shards::Tetrahedron<10>::key:
case shards::Tetrahedron<11>::key:
case shards::Hexahedron<20>::key:
case shards::Hexahedron<27>::key:
case shards::Pyramid<13>::key:
case shards::Pyramid<14>::key:
case shards::Wedge<15>::key:
case shards::Wedge<18>::key:
case shards::Pentagon<5>::key:
case shards::Hexagon<6>::key:
default:
shards::CellTopology topology(topology_data);
std::cout << "topology = " << topology.getName() << std::endl;
throw std::runtime_error("unknown/unhandled topology in JacobianUtil");
break;
} // end switch over element type
return metric_valid;
}
bool operator()(const stk::mesh::Entity& lhs, const stk::mesh::Entity& rhs) const
{
const stk::mesh::EntityKey lhs_key = lhs.key();
const stk::mesh::EntityKey rhs_key = rhs.key();
return lhs_key == rhs_key;
}