Albany::IossSTKMeshStruct::IossSTKMeshStruct(
const Teuchos::RCP<Teuchos::ParameterList>& params,
const Teuchos::RCP<Teuchos::ParameterList>& adaptParams_,
const Teuchos::RCP<const Epetra_Comm>& comm) :
GenericSTKMeshStruct(params, adaptParams_),
out(Teuchos::VerboseObjectBase::getDefaultOStream()),
useSerialMesh(false),
periodic(params->get("Periodic BC", false)),
m_hasRestartSolution(false),
m_restartDataTime(-1.0),
m_solutionFieldHistoryDepth(0)
{
params->validateParameters(*getValidDiscretizationParameters(),0);
mesh_data = new stk::io::MeshData();
usePamgen = (params->get("Method","Exodus") == "Pamgen");
std::vector<std::string> entity_rank_names;
// eMesh needs "FAMILY_TREE" entity
if(buildEMesh)
entity_rank_names.push_back("FAMILY_TREE");
#ifdef ALBANY_ZOLTAN // rebalance requires Zoltan
if (params->get<bool>("Use Serial Mesh", false) && comm->NumProc() > 1){
// We are parallel but reading a single exodus file
useSerialMesh = true;
readSerialMesh(comm, entity_rank_names);
}
else
#endif
if (!usePamgen) {
*out << "Albany_IOSS: Loading STKMesh from Exodus file "
<< params->get<std::string>("Exodus Input File Name") << std::endl;
stk::io::create_input_mesh("exodusii",
// create_input_mesh("exodusii",
params->get<std::string>("Exodus Input File Name"),
Albany::getMpiCommFromEpetraComm(*comm),
*metaData, *mesh_data,
entity_rank_names);
}
else {
*out << "Albany_IOSS: Loading STKMesh from Pamgen file "
<< params->get<std::string>("Pamgen Input File Name") << std::endl;
stk::io::create_input_mesh("pamgen",
// create_input_mesh("pamgen",
params->get<std::string>("Pamgen Input File Name"),
Albany::getMpiCommFromEpetraComm(*comm),
*metaData, *mesh_data,
entity_rank_names);
}
typedef Teuchos::Array<std::string> StringArray;
const StringArray additionalNodeSets = params->get("Additional Node Sets", StringArray());
for (StringArray::const_iterator it = additionalNodeSets.begin(), it_end = additionalNodeSets.end(); it != it_end; ++it) {
stk::mesh::Part &newNodeSet = metaData->declare_part(*it, metaData->node_rank());
if (!stk::io::is_part_io_part(newNodeSet)) {
stk::mesh::Field<double> * const distrFactorfield = metaData->get_field<stk::mesh::Field<double> >("distribution_factors");
stk::mesh::put_field(*distrFactorfield, metaData->node_rank(), newNodeSet);
stk::io::put_io_part_attribute(newNodeSet);
}
}
numDim = metaData->spatial_dimension();
stk::io::put_io_part_attribute(metaData->universal_part());
// Set element blocks, side sets and node sets
const stk::mesh::PartVector & all_parts = metaData->get_parts();
std::vector<std::string> ssNames;
std::vector<std::string> nsNames;
int numEB = 0;
for (stk::mesh::PartVector::const_iterator i = all_parts.begin();
i != all_parts.end(); ++i) {
stk::mesh::Part * const part = *i ;
if ( part->primary_entity_rank() == metaData->element_rank()) {
if (part->name()[0] != '{') {
//*out << "IOSS-STK: Element part \"" << part->name() << "\" found " << std::endl;
partVec[numEB] = part;
numEB++;
}
}
else if ( part->primary_entity_rank() == metaData->node_rank()) {
if (part->name()[0] != '{') {
//*out << "Mesh has Node Set ID: " << part->name() << std::endl;
nsPartVec[part->name()]=part;
nsNames.push_back(part->name());
}
}
else if ( part->primary_entity_rank() == metaData->side_rank()) {
if (part->name()[0] != '{') {
// print(*out, "Found side_rank entity:\n", *part);
ssPartVec[part->name()]=part;
}
}
}
cullSubsetParts(ssNames, ssPartVec); // Eliminate sidesets that are subsets of other sidesets
#if 0
// for debugging, print out the parts now
std::map<std::string, stk::mesh::Part*>::iterator it;
for(it = ssPartVec.begin(); it != ssPartVec.end(); ++it){ // loop over the parts in the map
// for each part in turn, get the name of parts that are a subset of it
print(*out, "Found \n", *it->second);
}
// end debugging
#endif
int cub = params->get("Cubature Degree",3);
int worksetSizeMax = params->get("Workset Size",50);
// Get number of elements per element block using Ioss for use
// in calculating an upper bound on the worksetSize.
std::vector<int> el_blocks;
stk::io::get_element_block_sizes(*mesh_data, el_blocks);
TEUCHOS_TEST_FOR_EXCEPT(el_blocks.size() != partVec.size());
int ebSizeMax = *std::max_element(el_blocks.begin(), el_blocks.end());
int worksetSize = this->computeWorksetSize(worksetSizeMax, ebSizeMax);
// Build a map to get the EB name given the index
for (int eb=0; eb<numEB; eb++)
this->ebNameToIndex[partVec[eb]->name()] = eb;
// Construct MeshSpecsStruct
if (!params->get("Separate Evaluators by Element Block",false)) {
const CellTopologyData& ctd = *metaData->get_cell_topology(*partVec[0]).getCellTopologyData();
this->meshSpecs[0] = Teuchos::rcp(new Albany::MeshSpecsStruct(ctd, numDim, cub,
nsNames, ssNames, worksetSize, partVec[0]->name(),
this->ebNameToIndex, this->interleavedOrdering));
}
else {
*out << "MULTIPLE Elem Block in Ioss: DO worksetSize[eb] max?? " << std::endl;
this->allElementBlocksHaveSamePhysics=false;
this->meshSpecs.resize(numEB);
for (int eb=0; eb<numEB; eb++) {
const CellTopologyData& ctd = *metaData->get_cell_topology(*partVec[eb]).getCellTopologyData();
this->meshSpecs[eb] = Teuchos::rcp(new Albany::MeshSpecsStruct(ctd, numDim, cub,
nsNames, ssNames, worksetSize, partVec[eb]->name(),
this->ebNameToIndex, this->interleavedOrdering));
std::cout << "el_block_size[" << eb << "] = " << el_blocks[eb] << " name " << partVec[eb]->name() << std::endl;
}
}
{
const Ioss::Region *inputRegion = mesh_data->m_input_region;
m_solutionFieldHistoryDepth = inputRegion->get_property("state_count").get_int();
}
}
Albany::IossSTKMeshStruct::IossSTKMeshStruct(
const Teuchos::RCP<Teuchos::ParameterList>& params,
const Teuchos::RCP<Teuchos::ParameterList>& adaptParams_,
const Teuchos::RCP<const Teuchos_Comm>& commT) :
GenericSTKMeshStruct(params, adaptParams_),
out(Teuchos::VerboseObjectBase::getDefaultOStream()),
useSerialMesh(false),
periodic(params->get("Periodic BC", false)),
m_hasRestartSolution(false),
m_restartDataTime(-1.0),
m_solutionFieldHistoryDepth(0)
{
params->validateParameters(*getValidDiscretizationParameters(),0);
usePamgen = (params->get("Method","Exodus") == "Pamgen");
const Teuchos::MpiComm<int>* mpiComm = dynamic_cast<const Teuchos::MpiComm<int>* > (commT.get());
std::vector<std::string> entity_rank_names = stk::mesh::entity_rank_names();
// eMesh needs "FAMILY_TREE" entity
if(buildEMesh) {
entity_rank_names.push_back("FAMILY_TREE");
}
const Teuchos::MpiComm<int>* theComm = dynamic_cast<const Teuchos::MpiComm<int>* > (commT.get());
if (params->get<bool>("Use Serial Mesh", false) && commT->getSize() > 1){
// We are parallel but reading a single exodus file
useSerialMesh = true;
// Read a single exodus mesh on Proc 0 then rebalance it across the machine
MPI_Group group_world;
MPI_Group peZero;
MPI_Comm peZeroComm;
//MPI_Comm theComm = Albany::getMpiCommFromEpetraComm(*comm);
int process_rank[1]; // the reader process
process_rank[0] = 0;
int my_rank = commT->getRank();
//get the group under theComm
MPI_Comm_group(*theComm->getRawMpiComm(), &group_world);
// create the new group. This group includes only processor zero - that is the only processor that reads the file
MPI_Group_incl(group_world, 1, process_rank, &peZero);
// create the new communicator - it just contains processor zero
MPI_Comm_create(*theComm->getRawMpiComm(), peZero, &peZeroComm);
mesh_data = Teuchos::rcp(new stk::io::StkMeshIoBroker(peZeroComm));
}
else {
mesh_data = Teuchos::rcp(new stk::io::StkMeshIoBroker(*theComm->getRawMpiComm()));
}
// Create input mesh
mesh_data->set_rank_name_vector(entity_rank_names);
mesh_data->set_sideset_face_creation_behavior(stk::io::StkMeshIoBroker::STK_IO_SIDESET_FACE_CREATION_CLASSIC);
//StkMeshIoBroker::set_sideset_face_creation_behavior(stk::io::StkMeshIoBroker::STK_IO_SIDESET_FACE_CREATION_CLASSIC);
std::string mesh_type;
std::string file_name;
if (!usePamgen) {
*out << "Albany_IOSS: Loading STKMesh from Exodus file "
<< params->get<std::string>("Exodus Input File Name") << std::endl;
mesh_type = "exodusII";
file_name = params->get<std::string>("Exodus Input File Name");
}
else {
*out << "Albany_IOSS: Loading STKMesh from Pamgen file "
<< params->get<std::string>("Pamgen Input File Name") << std::endl;
mesh_type = "pamgen";
file_name = params->get<std::string>("Pamgen Input File Name");
}
mesh_data->add_mesh_database(file_name, mesh_type, stk::io::READ_MESH);
mesh_data->create_input_mesh();
metaData = mesh_data->meta_data_rcp();
// End of creating input mesh
typedef Teuchos::Array<std::string> StringArray;
const StringArray additionalNodeSets = params->get("Additional Node Sets", StringArray());
for (StringArray::const_iterator it = additionalNodeSets.begin(), it_end = additionalNodeSets.end(); it != it_end; ++it) {
stk::mesh::Part &newNodeSet = metaData->declare_part(*it, stk::topology::NODE_RANK);
if (!stk::io::is_part_io_part(newNodeSet)) {
stk::mesh::Field<double> * const distrFactorfield = metaData->get_field<stk::mesh::Field<double> >(stk::topology::NODE_RANK, "distribution_factors");
stk::mesh::put_field(*distrFactorfield, newNodeSet);
stk::io::put_io_part_attribute(newNodeSet);
}
}
numDim = metaData->spatial_dimension();
stk::io::put_io_part_attribute(metaData->universal_part());
// Set element blocks, side sets and node sets
const stk::mesh::PartVector & all_parts = metaData->get_parts();
std::vector<std::string> ssNames;
std::vector<std::string> nsNames;
int numEB = 0;
for (stk::mesh::PartVector::const_iterator i = all_parts.begin();
i != all_parts.end(); ++i) {
stk::mesh::Part * const part = *i ;
if (!stk::mesh::is_auto_declared_part(*part)) {
if ( part->primary_entity_rank() == stk::topology::ELEMENT_RANK) {
//*out << "IOSS-STK: Element part \"" << part->name() << "\" found " << std::endl;
partVec[numEB] = part;
numEB++;
}
else if ( part->primary_entity_rank() == stk::topology::NODE_RANK) {
//*out << "Mesh has Node Set ID: " << part->name() << std::endl;
nsPartVec[part->name()]=part;
nsNames.push_back(part->name());
}
else if ( part->primary_entity_rank() == metaData->side_rank()) {
//print(*out, "Found side_rank entity:\n", *part);
ssPartVec[part->name()]=part;
}
}
}
cullSubsetParts(ssNames, ssPartVec); // Eliminate sidesets that are subsets of other sidesets
#if 0
// for debugging, print out the parts now
std::map<std::string, stk::mesh::Part*>::iterator it;
for(it = ssPartVec.begin(); it != ssPartVec.end(); ++it){ // loop over the parts in the map
// for each part in turn, get the name of parts that are a subset of it
print(*out, "Found \n", *it->second);
}
// end debugging
#endif
const int cub = params->get("Cubature Degree",3);
//Get Cubature Rule
const std::string cub_rule_string = params->get("Cubature Rule", "GAUSS");
Intrepid2::EIntrepidPLPoly cub_rule;
if (cub_rule_string == "GAUSS")
cub_rule = static_cast<Intrepid2::EIntrepidPLPoly>(Intrepid2::PL_GAUSS);
else if (cub_rule_string == "GAUSS_RADAU_LEFT")
cub_rule = static_cast<Intrepid2::EIntrepidPLPoly>(Intrepid2::PL_GAUSS_RADAU_LEFT);
else if (cub_rule_string == "GAUSS_RADAU_RIGHT")
cub_rule = static_cast<Intrepid2::EIntrepidPLPoly>(Intrepid2::PL_GAUSS_RADAU_RIGHT);
else if (cub_rule_string == "GAUSS_LOBATTO")
cub_rule = static_cast<Intrepid2::EIntrepidPLPoly>(Intrepid2::PL_GAUSS_LOBATTO);
else
TEUCHOS_TEST_FOR_EXCEPTION (true, Teuchos::Exceptions::InvalidParameterValue,
"Invalid Cubature Rule: " << cub_rule_string << "; valid options are GAUSS, GAUSS_RADAU_LEFT, GAUSS_RADAU_RIGHT, and GAUSS_LOBATTO");
int worksetSizeMax = params->get("Workset Size",50);
// Get number of elements per element block using Ioss for use
// in calculating an upper bound on the worksetSize.
std::vector<int> el_blocks;
get_element_block_sizes(*mesh_data, el_blocks);
TEUCHOS_TEST_FOR_EXCEPT(el_blocks.size() != partVec.size());
int ebSizeMax = *std::max_element(el_blocks.begin(), el_blocks.end());
int worksetSize = this->computeWorksetSize(worksetSizeMax, ebSizeMax);
// Build a map to get the EB name given the index
for (int eb=0; eb<numEB; eb++)
this->ebNameToIndex[partVec[eb]->name()] = eb;
// Construct MeshSpecsStruct
if (!params->get("Separate Evaluators by Element Block",false)) {
const CellTopologyData& ctd = *metaData->get_cell_topology(*partVec[0]).getCellTopologyData();
this->meshSpecs[0] = Teuchos::rcp(new Albany::MeshSpecsStruct(
ctd, numDim, cub, nsNames, ssNames, worksetSize, partVec[0]->name(),
this->ebNameToIndex, this->interleavedOrdering, false, cub_rule));
}
else {
*out << "MULTIPLE Elem Block in Ioss: DO worksetSize[eb] max?? " << std::endl;
this->allElementBlocksHaveSamePhysics=false;
this->meshSpecs.resize(numEB);
for (int eb=0; eb<numEB; eb++) {
const CellTopologyData& ctd = *metaData->get_cell_topology(*partVec[eb]).getCellTopologyData();
this->meshSpecs[eb] = Teuchos::rcp(new Albany::MeshSpecsStruct(
ctd, numDim, cub, nsNames, ssNames, worksetSize, partVec[eb]->name(),
this->ebNameToIndex, this->interleavedOrdering, true, cub_rule));
//std::cout << "el_block_size[" << eb << "] = " << el_blocks[eb] << " name " << partVec[eb]->name() << std::endl;
}
}
{
const Ioss::Region& inputRegion = *(mesh_data->get_input_io_region());
m_solutionFieldHistoryDepth = inputRegion.get_property("state_count").get_int();
}
}
