void Vertices::fillVertexIds(const stk::mesh::BulkData& bulkData,
const stk::mesh::EntityVector &entities)
{
mVertexIds.resize(entities.size(), 0);
for(size_t i=0;i<entities.size();++i)
mVertexIds[i] = bulkData.identifier(entities[i]);
}
void Vertices::fillFieldVertexWeights(const stk::balance::BalanceSettings& balanceSettings,
const stk::mesh::BulkData& stkMeshBulkData,
const std::vector<stk::mesh::Selector>& selectors,
const stk::mesh::EntityVector &entitiesToBalance)
{
unsigned numSelectors = selectors.size();
unsigned numEntities = entitiesToBalance.size();
unsigned numCriteria = balanceSettings.getNumCriteria();
mVertexWeights.resize(numSelectors*numEntities*numCriteria);
for (double &weight : mVertexWeights) { weight = 0.0; }
for(size_t i=0;i<entitiesToBalance.size();++i)
{
for (unsigned sel=0 ; sel<numSelectors ; ++sel)
{
stk::mesh::Selector selector = selectors[sel];
if (selector(stkMeshBulkData.bucket(entitiesToBalance[i])))
{
for(size_t weight_index=0;weight_index<numCriteria;weight_index++)
{
unsigned index = stk::balance::internal::get_index(numSelectors, numCriteria, i, sel, weight_index);
mVertexWeights[index] = balanceSettings.getGraphVertexWeight(entitiesToBalance[i], weight_index);;
}
}
}
}
}
void Vertices::fillCoordinates(const stk::mesh::BulkData& bulkData,
const std::string& coords_field_name,
const stk::mesh::EntityVector &entities)
{
mVertexCoordinates.resize(entities.size()*mSpatialDim, 0);
const stk::mesh::FieldBase * coord = bulkData.mesh_meta_data().get_field(stk::topology::NODE_RANK, coords_field_name);
for(size_t i=0;i<entities.size();++i)
stk::balance::internal::fillEntityCentroid(bulkData, coord, entities[i], &mVertexCoordinates[mSpatialDim*i]);
}
OrdinalAndPermutation
get_ordinal_and_permutation(const stk::mesh::BulkData& mesh, stk::mesh::Entity parent_entity, stk::mesh::EntityRank to_rank, const stk::mesh::EntityVector &nodes_of_sub_rank)
{
std::pair<stk::mesh::ConnectivityOrdinal, stk::mesh::Permutation> ordinalAndPermutation = std::make_pair(stk::mesh::INVALID_CONNECTIVITY_ORDINAL,
stk::mesh::INVALID_PERMUTATION);
unsigned nodes_of_sub_rank_size = nodes_of_sub_rank.size();
const Entity* elemNodes = mesh.begin_nodes(parent_entity);
stk::topology elemTopology = mesh.bucket(parent_entity).topology();
unsigned num_entities_of_sub_topology = elemTopology.num_sub_topology(to_rank);
unsigned max_nodes_possible = 100;
stk::mesh::EntityVector nodes_of_sub_topology;
nodes_of_sub_topology.reserve(max_nodes_possible);
std::pair<bool, unsigned> result;
for (unsigned i=0;i<num_entities_of_sub_topology;++i)
{
stk::topology sub_topology = elemTopology.sub_topology(to_rank, i);
unsigned num_nodes = sub_topology.num_nodes();
if (num_nodes != nodes_of_sub_rank_size)
{
continue;
}
ThrowRequireMsg(num_nodes == nodes_of_sub_rank.size(), "AHA! num_nodes != nodes_of_sub_rank.size()");
ThrowRequireMsg(num_nodes<=max_nodes_possible, "Program error. Exceeded expected array dimensions. Contact sierra-help for support.");
nodes_of_sub_topology.resize(num_nodes);
elemTopology.sub_topology_nodes(elemNodes, to_rank, i, nodes_of_sub_topology.begin());
if (!elemTopology.is_shell() || (to_rank == stk::topology::EDGE_RANK))
{
result = sub_topology.equivalent(nodes_of_sub_rank, nodes_of_sub_topology);
}
else
{
result = sub_topology.equivalent(nodes_of_sub_rank, nodes_of_sub_topology);
if (result.first && result.second >= sub_topology.num_positive_permutations())
{
result.first = false;
}
}
if (result.first == true)
{
ordinalAndPermutation.first = static_cast<stk::mesh::ConnectivityOrdinal>(i);
ordinalAndPermutation.second = static_cast<stk::mesh::Permutation>(result.second);
}
}
return ordinalAndPermutation;
}
void move_killed_elements_out_of_parts(stk::mesh::BulkData& bulkData,
const stk::mesh::EntityVector& killedElements,
const stk::mesh::PartVector& removeParts)
{
std::vector<stk::mesh::PartVector> add_parts(killedElements.size());
std::vector<stk::mesh::PartVector> rm_parts(killedElements.size());
for (size_t j=0;j<killedElements.size();++j)
{
rm_parts[j] = removeParts;
}
bulkData.batch_change_entity_parts(killedElements, add_parts, rm_parts);
}
void Vertices::fillVertexWeights(const stk::mesh::BulkData& bulkData,
const stk::balance::BalanceSettings& balanceSettings,
const stk::mesh::EntityVector &entities,
const std::vector<stk::mesh::Selector> &selectors)
{
if(balanceSettings.fieldSpecifiedVertexWeights())
{
fillFieldVertexWeights(balanceSettings, bulkData, selectors, entities);
}
else
{
mVertexWeights.resize(entities.size(), 0.0);
for(size_t i=0;i<entities.size();++i)
mVertexWeights[i] = balanceSettings.getGraphVertexWeight(bulkData.bucket(entities[i]).topology());
}
}
void add_locally_owned_side_from_element_side_pair(BulkData &bulkData, const SideSetEntry &facet, stk::mesh::EntityVector &sidesetSides, impl::SkinBoundaryErrorReporter &reporter)
{
Entity side = get_side_entity_for_element_side_pair(bulkData, facet);
if(bulkData.is_valid(side) && bulkData.bucket(side).owned())
{
sidesetSides.push_back(side);
reporter.add_entry(side, facet);
}
}
inline void deactivate_elements(const stk::mesh::EntityVector &deactivated_elems, stk::mesh::BulkData &bulkData, stk::mesh::Part& active)
{
bulkData.modification_begin();
for(size_t i = 0; i < deactivated_elems.size(); ++i)
{
bulkData.change_entity_parts(deactivated_elems[i], stk::mesh::PartVector(), stk::mesh::PartVector(1, &active));
}
bulkData.modification_end();
}
stk::mesh::EntityVector get_entity_vector_difference(const stk::mesh::EntityVector & A, const stk::mesh::EntityVector &B)
{
stk::mesh::EntityVector difference(A.size() + B.size());
stk::mesh::EntityVector::iterator it;
it = std::set_difference(A.begin(), A.end(), B.begin(), B.end(), difference.begin());
difference.resize(it - difference.begin());
return difference;
}
inline
size_t get_entities(stk::mesh::Part &part,
stk::mesh::EntityRank type,
const stk::mesh::BulkData &bulk,
stk::mesh::EntityVector &entities,
bool include_shared,
const stk::mesh::Selector *subset_selector)
{
stk::mesh::MetaData & meta = stk::mesh::MetaData::get(part);
stk::mesh::Selector own_share = meta.locally_owned_part();
if(include_shared)
own_share |= meta.globally_shared_part();
stk::mesh::Selector selector = part & own_share;
if(subset_selector)
selector &= *subset_selector;
get_selected_entities(selector, bulk.buckets(type), entities);
return entities.size();
}
void fill_sharing_data(stk::mesh::BulkData& bulkData, stk::mesh::ElemElemGraph &graph, const stk::mesh::EntityVector& sidesThatNeedFixing, std::vector<SideSharingData>& sideSharingDataThisProc, std::vector<stk::mesh::impl::IdViaSidePair>& idAndSides)
{
// Element 1, side 5: face 15
// Element 2, side 3: face 23
// Are these faces the same? Yes: delete face 23, then connect face 15 to element 2 with negative permutation
const stk::mesh::PartOrdinal sharedOrd = bulkData.mesh_meta_data().globally_shared_part().mesh_meta_data_ordinal();
for(size_t i=0;i<sidesThatNeedFixing.size();++i)
{
stk::mesh::impl::ElementViaSidePair elementAndSide = get_element_and_side_ordinal(bulkData, sidesThatNeedFixing[i]);
stk::mesh::impl::LocalId localElemId = graph.get_local_element_id(elementAndSide.element);
for(const stk::mesh::GraphEdge& edge : graph.get_edges_for_element(localElemId))
{
if(edge.side1() == elementAndSide.side && edge.elem2() < 0)
{
const stk::mesh::impl::ParallelInfo &pInfo = graph.get_parallel_info_for_graph_edge(edge);
const stk::mesh::Entity* nodes = bulkData.begin_nodes(sidesThatNeedFixing[i]);
unsigned numNodes = bulkData.num_nodes(sidesThatNeedFixing[i]);
SideSharingData localTemp({bulkData.identifier(elementAndSide.element), elementAndSide.side},
sidesThatNeedFixing[i],
pInfo.get_proc_rank_of_neighbor(),
std::min(bulkData.parallel_rank(),pInfo.get_proc_rank_of_neighbor()),
bulkData.identifier(sidesThatNeedFixing[i]));
localTemp.sideNodes.resize(numNodes);
for(unsigned j=0; j<numNodes; ++j) {
localTemp.sideNodes[j] = bulkData.identifier(nodes[j]);
}
fill_part_ordinals_besides_owned_and_shared(bulkData.bucket(sidesThatNeedFixing[i]), sharedOrd, localTemp.partOrdinals);
sideSharingDataThisProc.push_back(localTemp);
stk::mesh::EntityId localId = -edge.elem2();
idAndSides.push_back({localId, edge.side2()});
}
}
}
}
stk::mesh::Entity declare_element_to_sub_topology_with_nodes(stk::mesh::BulkData &mesh, stk::mesh::Entity elem, stk::mesh::EntityVector &sub_topology_nodes,
stk::mesh::EntityId global_sub_topology_id, stk::mesh::EntityRank to_rank, stk::mesh::Part &part)
{
std::pair<stk::mesh::ConnectivityOrdinal, stk::mesh::Permutation> ordinalAndPermutation = get_ordinal_and_permutation(mesh, elem, to_rank, sub_topology_nodes);
if ((ordinalAndPermutation.first == stk::mesh::ConnectivityOrdinal::INVALID_CONNECTIVITY_ORDINAL)
|| (ordinalAndPermutation.second == stk::mesh::Permutation::INVALID_PERMUTATION))
{
stk::mesh::Entity invalid;
invalid = stk::mesh::Entity::InvalidEntity;
return invalid;
}
stk::mesh::Entity side = mesh.declare_entity(to_rank, global_sub_topology_id, part);
for (unsigned i=0;i<sub_topology_nodes.size();++i)
{
mesh.declare_relation(side, sub_topology_nodes[i], i);
}
mesh.declare_relation(elem, side, ordinalAndPermutation.first, ordinalAndPermutation.second);
return side;
}
void find_ghosted_nodes_that_need_to_be_shared(const stk::mesh::BulkData & bulk, stk::mesh::EntityVector& ghosted_nodes_that_are_now_shared)
{
stk::mesh::EntityRank endRank = static_cast<stk::mesh::EntityRank>(bulk.mesh_meta_data().entity_rank_count());
if (endRank >= stk::topology::END_RANK)
{
endRank = stk::topology::END_RANK;
}
for (stk::mesh::EntityRank rank=stk::topology::EDGE_RANK; rank<endRank; ++rank)
{
const stk::mesh::BucketVector& entity_buckets = bulk.buckets(rank);
for(size_t i=0; i<entity_buckets.size(); ++i)
{
const stk::mesh::Bucket& bucket = *entity_buckets[i];
if ( bucket.owned() )
{
for(size_t n=0; n<bucket.size(); ++n)
{
const stk::mesh::Entity * nodes = bulk.begin_nodes(bucket[n]);
unsigned num_nodes = bulk.num_nodes(bucket[n]);
for (unsigned j=0;j<num_nodes;++j)
{
if (bulk.in_receive_ghost(bulk.entity_key(nodes[j])))
{
ghosted_nodes_that_are_now_shared.push_back(nodes[j]);
}
}
}
}
}
}
std::sort(ghosted_nodes_that_are_now_shared.begin(), ghosted_nodes_that_are_now_shared.end());
stk::mesh::EntityVector::iterator iter = std::unique(ghosted_nodes_that_are_now_shared.begin(), ghosted_nodes_that_are_now_shared.end());
ghosted_nodes_that_are_now_shared.erase(iter, ghosted_nodes_that_are_now_shared.end());
}
void fill_element_and_side_ids(Ioss::GroupingEntity & io,
stk::mesh::Part * const part,
const stk::mesh::BulkData & bulk_data,
stk::topology stk_element_topology,
const stk::mesh::Selector *subset_selector,
stk::mesh::EntityVector &sides,
std::vector<INT>& elem_side_ids)
{
if (bulk_data.has_sideset_data())
{
const stk::mesh::SideSet& sset = bulk_data.get_sideset_data(part->id());
size_t num_sides = sset.size();
elem_side_ids.reserve(num_sides*2);
stk::mesh::Selector selector = *part & ( bulk_data.mesh_meta_data().locally_owned_part() | bulk_data.mesh_meta_data().globally_shared_part() );
if(subset_selector)
selector &= *subset_selector;
for(size_t i=0;i<sset.size();++i)
{
stk::mesh::Entity element = sset[i].element;
stk::mesh::EntityId elemId = bulk_data.identifier(element);
int zero_based_side_ord = sset[i].side;
stk::mesh::Entity side = stk::mesh::get_side_entity_for_elem_id_side_pair_of_rank(bulk_data, elemId, zero_based_side_ord, bulk_data.mesh_meta_data().side_rank());
if(bulk_data.is_valid(side))
{
if(selector(bulk_data.bucket(side)))
{
if(bulk_data.bucket(element).topology() == stk_element_topology)
{
elem_side_ids.push_back(elemId);
elem_side_ids.push_back(zero_based_side_ord+1);
sides.push_back(side);
}
}
}
}
}
else
{
const stk::mesh::MetaData & meta_data = stk::mesh::MetaData::get(*part);
stk::mesh::EntityRank type = part_primary_entity_rank(*part);
size_t num_sides = get_entities(*part, type, bulk_data, sides, false, subset_selector);
elem_side_ids.reserve(num_sides * 2);
stk::mesh::EntityRank elem_rank = stk::topology::ELEMENT_RANK;
for(size_t i = 0; i < num_sides; ++i)
{
std::vector<stk::mesh::Entity> side;
side.push_back(sides[i]);
std::vector<stk::mesh::Entity> side_elements;
std::vector<stk::mesh::Entity> side_nodes(bulk_data.begin_nodes(sides[i]), bulk_data.end_nodes(sides[i]));
get_entities_through_relations(bulk_data, side_nodes, elem_rank, side_elements);
const size_t num_side_elem = side_elements.size();
std::sort(side_elements.begin(), side_elements.end(), stk::mesh::EntityLess(bulk_data));
stk::mesh::Entity suitable_elem = stk::mesh::Entity();
stk::mesh::ConnectivityOrdinal suitable_ordinal = stk::mesh::INVALID_CONNECTIVITY_ORDINAL;
for(size_t j = 0; j < num_side_elem; ++j)
{
const stk::mesh::Entity elem = side_elements[j];
const stk::mesh::Bucket &elemBucket = bulk_data.bucket(elem);
const bool isSelectingEverything = subset_selector == NULL;
const bool isElementBeingOutput = (isSelectingEverything || (*subset_selector)(elemBucket))
&& elemBucket.member(meta_data.locally_owned_part());
if(isElementBeingOutput)
{
const stk::mesh::Entity * elem_sides = bulk_data.begin(elem, type);
stk::mesh::ConnectivityOrdinal const * side_ordinal = bulk_data.begin_ordinals(elem, type);
const size_t num_elem_sides = bulk_data.num_connectivity(elem, type);
for(size_t k = 0; k < num_elem_sides; ++k)
{
if(elem_sides[k] == side[0])
{
suitable_elem = elem;
suitable_ordinal = side_ordinal[k];
break;
}
}
}
}
if(!bulk_data.is_valid(suitable_elem))
{
std::ostringstream oss;
oss << "ERROR, no suitable element found";
throw std::runtime_error(oss.str());
}
elem_side_ids.push_back(bulk_data.identifier(suitable_elem));
elem_side_ids.push_back(suitable_ordinal + 1); // Ioss is 1-based, mesh is 0-based.
}
}
}
stk::mesh::EntityVector get_elements_connected_to_all_nodes(const BulkDataFaceSharingTester& bulkData, const stk::mesh::EntityVector& nodes)
{
stk::mesh::EntityVector elements;
stk::mesh::impl::find_locally_owned_elements_these_nodes_have_in_common(bulkData, nodes.size(), nodes.data(), elements);
return elements;
}