void extract_sideset_data_from_io(std::vector<IdAndSideSet> &sidesetData)
{
stk::mesh::BulkData &bulk = this->bulk_data();
Ioss::Region *region = m_input_files[m_active_mesh_index]->get_input_io_region().get();
for ( const Ioss::SideSet * sset : region->get_sidesets() )
add_ioss_sideset_to_stk_sideset_with_sideset_id(bulk, sset, sidesetData);
}
void process_input_request(Ioss::Region ®ion,
stk::mesh::BulkData &bulk,
int step)
{
region.begin_state(step);
// Special processing for nodeblock (all nodes in model)...
const stk::mesh::MetaData& meta = stk::mesh::MetaData::get(bulk);
// ??? Get field data from nodeblock...
get_field_data(bulk, meta.universal_part(), stk::topology::NODE_RANK,
region.get_node_blocks()[0], Ioss::Field::TRANSIENT);
const stk::mesh::PartVector & all_parts = meta.get_parts();
for ( stk::mesh::PartVector::const_iterator
ip = all_parts.begin(); ip != all_parts.end(); ++ip ) {
stk::mesh::Part * const part = *ip;
const stk::mesh::EntityRank part_rank = part->primary_entity_rank();
// Check whether this part should be output to results database.
if (stk::io::is_part_io_part(*part)) {
// Get Ioss::GroupingEntity corresponding to this part...
Ioss::GroupingEntity *entity = region.get_entity(part->name());
if (entity != NULL) {
if (entity->type() == Ioss::SIDESET) {
Ioss::SideSet *sset = dynamic_cast<Ioss::SideSet*>(entity);
assert(sset != NULL);
int block_count = sset->block_count();
for (int i=0; i < block_count; i++) {
Ioss::SideBlock *side_block = sset->get_block(i);
/// \todo REFACTOR Need filtering mechanism.
get_field_data(bulk, *part,
part_rank,
side_block, Ioss::Field::TRANSIENT);
}
} else {
get_field_data(bulk, *part,
part_rank,
entity, Ioss::Field::TRANSIENT);
}
} else {
/// \todo IMPLEMENT handle error... Possibly an assert since
/// I think the corresponding entity should always exist...
}
}
}
region.end_state(step);
}
// ========================================================================
// Bulk Data
// ========================================================================
void process_nodeblocks(Ioss::Region ®ion, stk::mesh::BulkData &bulk)
{
// This must be called after the "process_element_blocks" call
// since there may be nodes that exist in the database that are
// not part of the analysis mesh due to subsetting of the element
// blocks.
const Ioss::NodeBlockContainer& node_blocks = region.get_node_blocks();
assert(node_blocks.size() == 1);
Ioss::NodeBlock *nb = node_blocks[0];
std::vector<stk::mesh::Entity> nodes;
stk::io::get_entity_list(nb, stk::topology::NODE_RANK, bulk, nodes);
/** \todo REFACTOR Application would probably store this field
* (and others) somewhere after the declaration instead of
* looking it up each time it is needed.
*/
const stk::mesh::MetaData& meta = stk::mesh::MetaData::get(bulk);
stk::mesh::Field<double,stk::mesh::Cartesian> *coord_field =
meta.get_field<stk::mesh::Field<double,stk::mesh::Cartesian> >(stk::topology::NODE_RANK, "coordinates");
stk::io::field_data_from_ioss(bulk, coord_field, nodes, nb, "mesh_model_coordinates");
}
// ========================================================================
void process_elementblocks(Ioss::Region ®ion, stk::mesh::BulkData &bulk)
{
const Ioss::ElementBlockContainer& elem_blocks = region.get_element_blocks();
for(Ioss::ElementBlockContainer::const_iterator it = elem_blocks.begin();
it != elem_blocks.end(); ++it) {
Ioss::ElementBlock *entity = *it;
if (stk::io::include_entity(entity)) {
const std::string &name = entity->name();
const stk::mesh::MetaData& meta = stk::mesh::MetaData::get(bulk);
stk::mesh::Part* const part = meta.get_part(name);
STKIORequire(part != NULL);
const stk::topology topo = part->topology();
if (topo == stk::topology::INVALID_TOPOLOGY) {
std::ostringstream msg ;
msg << " INTERNAL_ERROR: Part " << part->name() << " returned INVALID from get_topology()";
throw std::runtime_error( msg.str() );
}
std::vector<int> elem_ids ;
std::vector<int> connectivity ;
entity->get_field_data("ids", elem_ids);
entity->get_field_data("connectivity", connectivity);
size_t element_count = elem_ids.size();
int nodes_per_elem = topo.num_nodes();
stk::mesh::EntityIdVector connectivity2(nodes_per_elem);
std::vector<int>::const_iterator connBegin = connectivity.begin();
std::vector<stk::mesh::Entity> elements(element_count);
for(size_t i=0; i<element_count; ++i, connBegin += nodes_per_elem) {
std::copy(connBegin, connBegin + nodes_per_elem, connectivity2.begin());
elements[i] = stk::mesh::declare_element(bulk, *part, elem_ids[i], connectivity2);
}
// For this example, we are just taking all attribute fields
// found on the io database and populating fields on the
// corresponding mesh part. In practice, would probably be
// selective about which attributes to use...
Ioss::NameList names;
entity->field_describe(Ioss::Field::ATTRIBUTE, &names);
for (Ioss::NameList::const_iterator I = names.begin(); I != names.end(); ++I) {
if (*I == "attribute" && names.size() > 1)
continue;
stk::mesh::FieldBase *field = meta.get_field<stk::mesh::FieldBase>(stk::topology::ELEMENT_RANK, *I);
stk::io::field_data_from_ioss(bulk, field, elements, entity, *I);
}
}
}
}
// ========================================================================
void process_sidesets(Ioss::Region ®ion, stk::mesh::BulkData &bulk)
{
const Ioss::SideSetContainer& side_sets = region.get_sidesets();
for(Ioss::SideSetContainer::const_iterator it = side_sets.begin();
it != side_sets.end(); ++it) {
Ioss::SideSet *entity = *it;
if (stk::io::include_entity(entity)) {
process_surface_entity(entity, bulk);
}
}
}
// ========================================================================
void process_sidesets(Ioss::Region ®ion, stk::mesh::MetaData &meta)
{
const stk::mesh::EntityRank side_rank = meta.side_rank();
const Ioss::SideSetContainer& side_sets = region.get_sidesets();
stk::io::default_part_processing(side_sets, meta, side_rank);
for(Ioss::SideSetContainer::const_iterator it = side_sets.begin();
it != side_sets.end(); ++it) {
Ioss::SideSet *entity = *it;
if (stk::io::include_entity(entity)) {
process_surface_entity(entity, meta, side_rank);
}
}
}
// ========================================================================
void process_nodesets(Ioss::Region ®ion, stk::mesh::BulkData &bulk)
{
// Should only process nodes that have already been defined via the element
// blocks connectivity lists.
const Ioss::NodeSetContainer& node_sets = region.get_nodesets();
for(Ioss::NodeSetContainer::const_iterator it = node_sets.begin();
it != node_sets.end(); ++it) {
Ioss::NodeSet *entity = *it;
if (stk::io::include_entity(entity)) {
const std::string & name = entity->name();
const stk::mesh::MetaData& meta = stk::mesh::MetaData::get(bulk);
stk::mesh::Part* const part = meta.get_part(name);
STKIORequire(part != NULL);
stk::mesh::PartVector add_parts( 1 , part );
std::vector<int> node_ids ;
int node_count = entity->get_field_data("ids", node_ids);
std::vector<stk::mesh::Entity> nodes(node_count);
for(int i=0; i<node_count; ++i) {
nodes[i] = bulk.get_entity( stk::topology::NODE_RANK, node_ids[i] );
if (bulk.is_valid(nodes[i])) {
bulk.declare_entity(stk::topology::NODE_RANK, node_ids[i], add_parts );
}
}
/** \todo REFACTOR Application would probably store this field
* (and others) somewhere after the declaration instead of
* looking it up each time it is needed.
*/
stk::mesh::Field<double> *df_field =
meta.get_field<stk::mesh::Field<double> >(stk::topology::NODE_RANK, "distribution_factors");
if (df_field != NULL) {
stk::io::field_data_from_ioss(bulk, df_field, nodes, entity, "distribution_factors");
}
}
}
}
// ========================================================================
void process_nodesets(Ioss::Region ®ion, stk::mesh::MetaData &meta)
{
const Ioss::NodeSetContainer& node_sets = region.get_nodesets();
stk::io::default_part_processing(node_sets, meta, stk::topology::NODE_RANK);
/** \todo REFACTOR should "distribution_factor" be a default field
* that is automatically declared on all objects that it exists
* on as is done in current framework?
*/
stk::mesh::Field<double> & distribution_factors_field =
meta.declare_field<stk::mesh::Field<double> >(stk::topology::NODE_RANK, "distribution_factors");
/** \todo REFACTOR How to associate distribution_factors field
* with the nodeset part if a node is a member of multiple
* nodesets
*/
for(Ioss::NodeSetContainer::const_iterator it = node_sets.begin();
it != node_sets.end(); ++it) {
Ioss::NodeSet *entity = *it;
if (stk::io::include_entity(entity)) {
stk::mesh::Part* const part = meta.get_part(entity->name());
STKIORequire(part != NULL);
STKIORequire(entity->field_exists("distribution_factors"));
stk::mesh::put_field(distribution_factors_field, *part);
/** \todo IMPLEMENT truly handle fields... For this case we
* are just defining a field for each transient field that is
* present in the mesh...
*/
stk::io::define_io_fields(entity, Ioss::Field::TRANSIENT,
*part,
part->primary_entity_rank() ) ;
}
}
}
// ========================================================================
void process_elementblocks(Ioss::Region ®ion, stk::mesh::MetaData &meta)
{
const stk::mesh::EntityRank element_rank = stk::topology::ELEMENT_RANK;
const Ioss::ElementBlockContainer& elem_blocks = region.get_element_blocks();
stk::io::default_part_processing(elem_blocks, meta, element_rank);
// Parts were created above, now handle element block specific
// information (topology, attributes, ...);
for(Ioss::ElementBlockContainer::const_iterator it = elem_blocks.begin();
it != elem_blocks.end(); ++it) {
Ioss::ElementBlock *entity = *it;
if (stk::io::include_entity(entity)) {
stk::mesh::Part* const part = meta.get_part(entity->name());
STKIORequire(part != NULL);
const stk::mesh::EntityRank part_rank = part->primary_entity_rank();
// Element Block attributes (if any)...
/** \todo IMPLEMENT truly handle attribute fields... For this
* case we are just defining a field for each attribute field
* that is present in the mesh...
*/
stk::io::define_io_fields(entity, Ioss::Field::ATTRIBUTE,
*part,
part_rank);
/** \todo IMPLEMENT truly handle fields... For this case we
* are just defining a field for each transient field that is
* present in the mesh...
*/
stk::io::define_io_fields(entity, Ioss::Field::TRANSIENT,
*part,
part_rank);
}
}
}
// ========================================================================
void process_nodeblocks(Ioss::Region ®ion, stk::mesh::MetaData &meta)
{
const Ioss::NodeBlockContainer& node_blocks = region.get_node_blocks();
assert(node_blocks.size() == 1);
Ioss::NodeBlock *nb = node_blocks[0];
assert(nb->field_exists("mesh_model_coordinates"));
Ioss::Field coordinates = nb->get_field("mesh_model_coordinates");
int spatial_dim = coordinates.transformed_storage()->component_count();
stk::mesh::Field<double,stk::mesh::Cartesian> & coord_field =
meta.declare_field<stk::mesh::Field<double,stk::mesh::Cartesian> >(stk::topology::NODE_RANK, "coordinates");
stk::mesh::put_field( coord_field, meta.universal_part(),
spatial_dim);
/** \todo IMPLEMENT truly handle fields... For this case we are
* just defining a field for each transient field that is present
* in the mesh...
*/
stk::io::define_io_fields(nb, Ioss::Field::TRANSIENT, meta.universal_part(),stk::topology::NODE_RANK);
}
void
Albany::IossSTKMeshStruct::setFieldAndBulkData(
const Teuchos::RCP<const Epetra_Comm>& comm,
const Teuchos::RCP<Teuchos::ParameterList>& params,
const unsigned int neq_,
const AbstractFieldContainer::FieldContainerRequirements& req,
const Teuchos::RCP<Albany::StateInfoStruct>& sis,
const unsigned int worksetSize)
{
this->SetupFieldData(comm, neq_, req, sis, worksetSize);
*out << "IOSS-STK: number of node sets = " << nsPartVec.size() << std::endl;
*out << "IOSS-STK: number of side sets = " << ssPartVec.size() << std::endl;
metaData->commit();
// Restart index to read solution from exodus file.
int index = params->get("Restart Index",-1); // Default to no restart
double res_time = params->get<double>("Restart Time",-1.0); // Default to no restart
Ioss::Region *region = mesh_data->m_input_region;
/*
* The following code block reads a single mesh on PE 0, then distributes the mesh across
* the other processors. stk_rebalance is used, which requires Zoltan
*
* This code is only compiled if ALBANY_MPI and ALBANY_ZOLTAN are true
*/
#ifdef ALBANY_ZOLTAN // rebalance needs Zoltan
if(useSerialMesh){
bulkData->modification_begin();
if(comm->MyPID() == 0){ // read in the mesh on PE 0
stk::io::process_mesh_bulk_data(region, *bulkData);
// Read solution from exodus file.
if (index >= 0) { // User has specified a time step to restart at
*out << "Restart Index set, reading solution index : " << index << std::endl;
stk::io::input_mesh_fields(region, *bulkData, index);
m_restartDataTime = region->get_state_time(index);
m_hasRestartSolution = true;
}
else if (res_time >= 0) { // User has specified a time to restart at
*out << "Restart solution time set, reading solution time : " << res_time << std::endl;
stk::io::input_mesh_fields(region, *bulkData, res_time);
m_restartDataTime = res_time;
m_hasRestartSolution = true;
}
else {
*out << "Neither restart index or time are set. Not reading solution data from exodus file"<< std::endl;
}
}
bulkData->modification_end();
} // End UseSerialMesh - reading mesh on PE 0
else
#endif
/*
* The following code block reads a single mesh when Albany is compiled serially, or a
* Nemspread fileset if ALBANY_MPI is true.
*
*/
{ // running in Serial or Parallel read from Nemspread files
stk::io::populate_bulk_data(*bulkData, *mesh_data);
if (!usePamgen) {
// Read solution from exodus file.
if (index >= 0) { // User has specified a time step to restart at
*out << "Restart Index set, reading solution index : " << index << std::endl;
stk::io::process_input_request(*mesh_data, *bulkData, index);
m_restartDataTime = region->get_state_time(index);
m_hasRestartSolution = true;
}
else if (res_time >= 0) { // User has specified a time to restart at
*out << "Restart solution time set, reading solution time : " << res_time << std::endl;
stk::io::process_input_request(*mesh_data, *bulkData, res_time);
m_restartDataTime = res_time;
m_hasRestartSolution = true;
}
else {
*out << "Restart Index not set. Not reading solution from exodus ("
<< index << ")"<< std::endl;
}
}
bulkData->modification_end();
} // End Parallel Read - or running in serial
if(m_hasRestartSolution){
Teuchos::Array<std::string> default_field;
default_field.push_back("solution");
Teuchos::Array<std::string> restart_fields =
params->get<Teuchos::Array<std::string> >("Restart Fields", default_field);
// Get the fields to be used for restart
// See what state data was initialized from the stk::io request
// This should be propagated into stk::io
const Ioss::ElementBlockContainer& elem_blocks = region->get_element_blocks();
/*
// Uncomment to print what fields are in the exodus file
Ioss::NameList exo_fld_names;
elem_blocks[0]->field_describe(&exo_fld_names);
for(std::size_t i = 0; i < exo_fld_names.size(); i++){
*out << "Found field \"" << exo_fld_names[i] << "\" in exodus file" << std::endl;
}
*/
for (std::size_t i=0; i<sis->size(); i++) {
Albany::StateStruct& st = *((*sis)[i]);
if(elem_blocks[0]->field_exists(st.name))
for(std::size_t j = 0; j < restart_fields.size(); j++)
if(boost::iequals(st.name, restart_fields[j])){
*out << "Restarting from field \"" << st.name << "\" found in exodus file." << std::endl;
st.restartDataAvailable = true;
break;
}
}
}
// coordinates_field = metaData->get_field<VectorFieldType>(std::string("coordinates"));
//#ifdef ALBANY_FELIX
// surfaceHeight_field = metaData->get_field<ScalarFieldType>(std::string("surface height"));
//#endif
// Refine the mesh before starting the simulation if indicated
uniformRefineMesh(comm);
// Rebalance the mesh before starting the simulation if indicated
rebalanceInitialMesh(comm);
// Build additional mesh connectivity needed for mesh fracture (if indicated)
computeAddlConnectivity();
}