Albany::OrdinarySTKFieldContainer<Interleaved>::OrdinarySTKFieldContainer(
const Teuchos::RCP<Teuchos::ParameterList>& params_,
const Teuchos::RCP<stk::mesh::MetaData>& metaData_,
const Teuchos::RCP<stk::mesh::BulkData>& bulkData_,
const int neq_,
const AbstractFieldContainer::FieldContainerRequirements& req,
const int numDim_,
const Teuchos::RCP<Albany::StateInfoStruct>& sis)
: GenericSTKFieldContainer<Interleaved>(params_, metaData_, bulkData_, neq_, numDim_),
buildSphereVolume(false) {
typedef typename AbstractSTKFieldContainer::VectorFieldType VFT;
typedef typename AbstractSTKFieldContainer::ScalarFieldType SFT;
typedef typename AbstractSTKFieldContainer::SphereVolumeFieldType SVFT;
int num_time_deriv = params_->get<int>("Number Of Time Derivatives");
//Start STK stuff
this->coordinates_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, "coordinates");
stk::mesh::put_field(*this->coordinates_field , metaData_->universal_part(), numDim_);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*this->coordinates_field, Ioss::Field::MESH);
#endif
solution_field.resize(num_time_deriv + 1);
solution_field_dtk.resize(num_time_deriv + 1);
for(int num_vecs = 0; num_vecs <= num_time_deriv; num_vecs++){
solution_field[num_vecs] = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK,
params_->get<std::string>(sol_tag_name[num_vecs], sol_id_name[num_vecs]));
stk::mesh::put_field(*solution_field[num_vecs] , metaData_->universal_part(), neq_);
#if defined(ALBANY_DTK)
solution_field_dtk[num_vecs] = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK,
params_->get<std::string>(res_tag_name[num_vecs], sol_dtk_id_name[num_vecs]));
stk::mesh::put_field(*solution_field_dtk[num_vecs] , metaData_->universal_part() , neq_);
#endif
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*solution_field[num_vecs], Ioss::Field::TRANSIENT);
#if defined(ALBANY_DTK)
stk::io::set_field_role(*solution_field_dtk[num_vecs], Ioss::Field::TRANSIENT);
#endif
#endif
}
#if defined(ALBANY_LCM)
residual_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK,
params_->get<std::string>(res_tag_name[0], res_id_name[0]));
stk::mesh::put_field(*residual_field, metaData_->universal_part() , neq_);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*residual_field, Ioss::Field::TRANSIENT);
#endif
#endif
#if defined(ALBANY_LCM) && defined(ALBANY_SEACAS)
// sphere volume is a mesh attribute read from a genesis mesh file containing sphere element (used for peridynamics)
bool hasSphereVolumeFieldContainerRequirement = (std::find(req.begin(), req.end(), "Sphere Volume") != req.end());
if(hasSphereVolumeFieldContainerRequirement){
this->sphereVolume_field = metaData_->template get_field< SVFT >(stk::topology::ELEMENT_RANK, "volume");
if(this->sphereVolume_field != 0){
buildSphereVolume = true;
stk::io::set_field_role(*this->sphereVolume_field, Ioss::Field::ATTRIBUTE);
}
}
#endif
// If the problem requests that the initial guess at the solution equals the input node coordinates,
// set that here
/*
if(std::find(req.begin(), req.end(), "Initial Guess Coords") != req.end()){
this->copySTKField(this->coordinates_field, solution_field);
}
*/
this->addStateStructs(sis);
initializeSTKAdaptation();
}
void Albany::ExtrudedSTKMeshStruct::setFieldAndBulkData(
const Teuchos::RCP<const Teuchos_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)
{
int numLayers = params->get("NumLayers", 10);
bool useGlimmerSpacing = params->get("Use Glimmer Spacing", false);
GO maxGlobalElements2D = 0;
GO maxGlobalVertices2dId = 0;
GO numGlobalVertices2D = 0;
GO maxGlobalEdges2D = 0;
bool Ordering = params->get("Columnwise Ordering", false);
bool isTetra = true;
stk::mesh::BulkData& bulkData2D = *basalMeshStruct->bulkData;
stk::mesh::MetaData& metaData2D = *basalMeshStruct->metaData; //bulkData2D.mesh_meta_data();
std::vector<double> levelsNormalizedThickness(numLayers + 1), temperatureNormalizedZ, flowRateNormalizedZ;
if(useGlimmerSpacing)
for (int i = 0; i < numLayers+1; i++)
levelsNormalizedThickness[numLayers-i] = 1.0- (1.0 - std::pow(double(i) / numLayers + 1.0, -2))/(1.0 - std::pow(2.0, -2));
else //uniform layers
for (int i = 0; i < numLayers+1; i++)
levelsNormalizedThickness[i] = double(i) / numLayers;
Teuchos::ArrayRCP<double> layerThicknessRatio(numLayers), layersNormalizedThickness(numLayers);
for (int i = 0; i < numLayers; i++) {
layerThicknessRatio[i] = levelsNormalizedThickness[i+1]-levelsNormalizedThickness[i];
layersNormalizedThickness[i] = 0.5*(levelsNormalizedThickness[i]+levelsNormalizedThickness[i+1]);
}
/*std::cout<< "Levels: ";
for (int i = 0; i < numLayers+1; i++)
std::cout<< levelsNormalizedThickness[i] << " ";
std::cout<< "\n";*/
stk::mesh::Selector select_owned_in_part = stk::mesh::Selector(metaData2D.universal_part()) & stk::mesh::Selector(metaData2D.locally_owned_part());
stk::mesh::Selector select_overlap_in_part = stk::mesh::Selector(metaData2D.universal_part()) & (stk::mesh::Selector(metaData2D.locally_owned_part()) | stk::mesh::Selector(metaData2D.globally_shared_part()));
stk::mesh::Selector select_edges = stk::mesh::Selector(*metaData2D.get_part("LateralSide")) & (stk::mesh::Selector(metaData2D.locally_owned_part()) | stk::mesh::Selector(metaData2D.globally_shared_part()));
std::vector<stk::mesh::Entity> cells2D;
stk::mesh::get_selected_entities(select_overlap_in_part, bulkData2D.buckets(stk::topology::ELEMENT_RANK), cells2D);
std::vector<stk::mesh::Entity> nodes2D;
stk::mesh::get_selected_entities(select_overlap_in_part, bulkData2D.buckets(stk::topology::NODE_RANK), nodes2D);
std::vector<stk::mesh::Entity> edges2D;
stk::mesh::get_selected_entities(select_edges, bulkData2D.buckets(metaData2D.side_rank()), edges2D);
GO maxOwnedElements2D(0), maxOwnedNodes2D(0), maxOwnedSides2D(0), numOwnedNodes2D(0);
for (int i = 0; i < cells2D.size(); i++)
maxOwnedElements2D = std::max(maxOwnedElements2D, (GO) bulkData2D.identifier(cells2D[i]));
for (int i = 0; i < nodes2D.size(); i++)
maxOwnedNodes2D = std::max(maxOwnedNodes2D, (GO) bulkData2D.identifier(nodes2D[i]));
for (int i = 0; i < edges2D.size(); i++)
maxOwnedSides2D = std::max(maxOwnedSides2D, (GO) bulkData2D.identifier(edges2D[i]));
numOwnedNodes2D = stk::mesh::count_selected_entities(select_owned_in_part, bulkData2D.buckets(stk::topology::NODE_RANK));
//WARNING Currently GO == long int. For gcc compiler, long == long long, however this might not be true with other compilers.
//comm->MaxAll(&maxOwnedElements2D, &maxGlobalElements2D, 1);
Teuchos::reduceAll<int, GO>(*comm, Teuchos::REDUCE_MAX, maxOwnedElements2D, Teuchos::ptr(&maxGlobalElements2D));
//comm->MaxAll(&maxOwnedNodes2D, &maxGlobalVertices2dId, 1);
Teuchos::reduceAll<int, GO>(*comm, Teuchos::REDUCE_MAX, maxOwnedNodes2D, Teuchos::ptr(&maxGlobalVertices2dId));
//comm->MaxAll(&maxOwnedSides2D, &maxGlobalEdges2D, 1);
Teuchos::reduceAll<int, GO>(*comm, Teuchos::REDUCE_MAX, maxOwnedSides2D, Teuchos::ptr(&maxGlobalEdges2D));
//comm->SumAll(&numOwnedNodes2D, &numGlobalVertices2D, 1);
//The following should not be int int...
Teuchos::reduceAll<int, GO>(*comm, Teuchos::REDUCE_SUM, 1, &numOwnedNodes2D, &numGlobalVertices2D);
if (comm->getRank() == 0) std::cout << "Importing ascii files ...";
//std::cout << "Num Global Elements: " << maxGlobalElements2D<< " " << maxGlobalVertices2dId<< " " << maxGlobalEdges2D << std::endl;
Teuchos::Array<GO> indices(nodes2D.size());
for (int i = 0; i < nodes2D.size(); ++i)
indices[i] = bulkData2D.identifier(nodes2D[i]) - 1;
Teuchos::RCP<const Tpetra_Map>
nodes_map = Tpetra::createNonContigMapWithNode<LO, GO> (
indices(), comm, KokkosClassic::Details::getNode<KokkosNode>());
int numMyElements = (comm->getRank() == 0) ? numGlobalVertices2D : 0;
//Teuchos::RCP<const Tpetra_Map> serial_nodes_map = Tpetra::createUniformContigMap<LO, GO>(numMyElements, comm);
Teuchos::RCP<const Tpetra_Map> serial_nodes_map = Teuchos::rcp(new const Tpetra_Map(INVALID, numMyElements, 0, comm));
Teuchos::RCP<Tpetra_Import> importOperator = Teuchos::rcp(new Tpetra_Import(serial_nodes_map, nodes_map));
Teuchos::RCP<Tpetra_Vector> temp = Teuchos::rcp(new Tpetra_Vector(serial_nodes_map));
Teuchos::RCP<Tpetra_Vector> sHeightVec;
Teuchos::RCP<Tpetra_Vector> thickVec;
Teuchos::RCP<Tpetra_Vector> bTopographyVec;
Teuchos::RCP<Tpetra_Vector> bFrictionVec;
Teuchos::RCP<Tpetra_MultiVector> temperatureVecInterp;
Teuchos::RCP<Tpetra_MultiVector> flowRateVecInterp;
Teuchos::RCP<Tpetra_MultiVector> sVelocityVec;
Teuchos::RCP<Tpetra_MultiVector> velocityRMSVec;
bool hasSurface_height = std::find(req.begin(), req.end(), "surface_height") != req.end();
{
sHeightVec = Teuchos::rcp(new Tpetra_Vector(nodes_map));
std::string fname = params->get<std::string>("Surface Height File Name", "surface_height.ascii");
read2DFileSerial(fname, temp, comm);
sHeightVec->doImport(*temp, *importOperator, Tpetra::INSERT);
}
Teuchos::ArrayRCP<const ST> sHeightVec_constView = sHeightVec->get1dView();
bool hasThickness = std::find(req.begin(), req.end(), "thickness") != req.end();
{
std::string fname = params->get<std::string>("Thickness File Name", "thickness.ascii");
read2DFileSerial(fname, temp, comm);
thickVec = Teuchos::rcp(new Tpetra_Vector(nodes_map));
thickVec->doImport(*temp, *importOperator, Tpetra::INSERT);
}
Teuchos::ArrayRCP<const ST> thickVec_constView = thickVec->get1dView();
bool hasBed_topography = std::find(req.begin(), req.end(), "bed_topography") != req.end();
{
std::string fname = params->get<std::string>("Bed Topography File Name", "bed_topography.ascii");
read2DFileSerial(fname, temp, comm);
bTopographyVec = Teuchos::rcp(new Tpetra_Vector(nodes_map));
bTopographyVec->doImport(*temp, *importOperator, Tpetra::INSERT);
}
Teuchos::ArrayRCP<const ST> bTopographyVec_constView = bTopographyVec->get1dView();
bool hasBasal_friction = std::find(req.begin(), req.end(), "basal_friction") != req.end();
if(hasBasal_friction)
{
bFrictionVec = Teuchos::rcp(new Tpetra_Vector(nodes_map));
if (params->isParameter("Basal Friction File Name"))
{
std::string fname = params->get<std::string>("Basal Friction File Name", "basal_friction.ascii");
read2DFileSerial(fname, temp, comm);
bFrictionVec->doImport(*temp, *importOperator, Tpetra::INSERT);
}
else
{
// Try to load it from the 2D mesh
Albany::AbstractSTKFieldContainer::ScalarFieldType* field = 0;
field = metaData2D.get_field<Albany::AbstractSTKFieldContainer::ScalarFieldType>(stk::topology::NODE_RANK, "basal_friction");
if (field!=0)
{
Teuchos::ArrayRCP<ST> bFrictionVec_view = bFrictionVec->get1dViewNonConst();
stk::mesh::Entity node;
stk::mesh::EntityId nodeId;
int lid;
double* values;
//Now we have to stuff the vector in the mesh data
for (int i(0); i<nodes2D.size(); ++i)
{
nodeId = bulkData2D.identifier(nodes2D[i]) - 1;
lid = nodes_map->getLocalElement((GO)(nodeId));
values = stk::mesh::field_data(*field, nodes2D[i]);
bFrictionVec_view[lid] = values[0];
}
}
else
{
// We use a zero vector, but we issue a warning. Just in case the user forgot to setup something
std::cout << "No file name specified for 'basal_friction', and no field retrieved from the mesh. Using a zero vector.\n";
}
}
}
bool hasFlowRate = true;//std::find(req.begin(), req.end(), "flowRate") != req.end();
if(hasFlowRate) {
Teuchos::RCP<Tpetra_MultiVector> flowRateVec;
flowRateVecInterp = Teuchos::rcp(new Tpetra_MultiVector(nodes_map, numLayers));
std::string fname = params->get<std::string>("Flow Rate File Name", "flow_rate.ascii");
int err = readFileSerial(fname, serial_nodes_map, nodes_map, importOperator, flowRateVec, flowRateNormalizedZ, comm);
if(err == 0) {
int il0, il1, verticalTSize(flowRateVec->getNumVectors());
double h0(0.0);
for (int il = 0; il < numLayers; il++) {
if (layersNormalizedThickness[il] <= flowRateNormalizedZ[0]) {
il0 = 0;
il1 = 0;
h0 = 1.0;
}
else if (layersNormalizedThickness[il] >= flowRateNormalizedZ[verticalTSize - 1]) {
il0 = verticalTSize - 1;
il1 = verticalTSize - 1;
h0 = 0.0;
}
else {
int k = 0;
while (layersNormalizedThickness[il] > flowRateNormalizedZ[++k])
;
il0 = k - 1;
il1 = k;
h0 = (flowRateNormalizedZ[il1] - layersNormalizedThickness[il]) / (flowRateNormalizedZ[il1] - flowRateNormalizedZ[il0]);
}
Teuchos::ArrayRCP<ST> flowRateVecInterp_nonConstView = flowRateVecInterp->getVectorNonConst(il)->get1dViewNonConst();
Teuchos::ArrayRCP<const ST> flowRateVec_constView_il0 = flowRateVec->getVectorNonConst(il0)->get1dView();
Teuchos::ArrayRCP<const ST> flowRateVec_constView_il1 = flowRateVec->getVectorNonConst(il1)->get1dView();
for (int i = 0; i < nodes_map->getNodeNumElements(); i++)
flowRateVecInterp_nonConstView[i] = h0 * flowRateVec_constView_il0[i] + (1.0 - h0) * flowRateVec_constView_il1[i];
}
}
else hasFlowRate=false;
}
bool hasTemperature = std::find(req.begin(), req.end(), "temperature") != req.end();
if(hasTemperature) {
Teuchos::RCP<Tpetra_MultiVector> temperatureVec;
temperatureVecInterp = Teuchos::rcp(new Tpetra_MultiVector(nodes_map, numLayers + 1));
std::string fname = params->get<std::string>("Temperature File Name", "temperature.ascii");
int err = readFileSerial(fname, serial_nodes_map, nodes_map, importOperator, temperatureVec, temperatureNormalizedZ, comm);
if(err == 0) {
int il0, il1, verticalTSize(temperatureVec->getNumVectors());
double h0(0.0);
for (int il = 0; il < numLayers + 1; il++) {
if (levelsNormalizedThickness[il] <= temperatureNormalizedZ[0]) {
il0 = 0;
il1 = 0;
h0 = 1.0;
}
else if (levelsNormalizedThickness[il] >= temperatureNormalizedZ[verticalTSize - 1]) {
il0 = verticalTSize - 1;
il1 = verticalTSize - 1;
h0 = 0.0;
}
else {
int k = 0;
while (levelsNormalizedThickness[il] > temperatureNormalizedZ[++k])
;
il0 = k - 1;
il1 = k;
h0 = (temperatureNormalizedZ[il1] - levelsNormalizedThickness[il]) / (temperatureNormalizedZ[il1] - temperatureNormalizedZ[il0]);
}
Teuchos::ArrayRCP<ST> temperatureVecInterp_nonConstView = temperatureVecInterp->getVectorNonConst(il)->get1dViewNonConst();
Teuchos::ArrayRCP<const ST> temperatureVec_constView_il0 = temperatureVec->getVectorNonConst(il0)->get1dView();
Teuchos::ArrayRCP<const ST> temperatureVec_constView_il1 = temperatureVec->getVectorNonConst(il1)->get1dView();
for (int i = 0; i < nodes_map->getNodeNumElements(); i++)
temperatureVecInterp_nonConstView[i] = h0 * temperatureVec_constView_il0[i] + (1.0 - h0) * temperatureVec_constView_il1[i];
}
}
else hasTemperature = false;
}
Tpetra_MultiVector tempSV(serial_nodes_map,neq_);
bool hasSurfaceVelocity = std::find(req.begin(), req.end(), "surface_velocity") != req.end();
if(hasSurfaceVelocity) {
std::string fname = params->get<std::string>("Surface Velocity File Name", "surface_velocity.ascii");
readFileSerial(fname, tempSV, comm);
sVelocityVec = Teuchos::rcp(new Tpetra_MultiVector (nodes_map, neq_));
sVelocityVec->doImport(tempSV, *importOperator, Tpetra::INSERT);
}
bool hasSurfaceVelocityRMS = std::find(req.begin(), req.end(), "surface_velocity_rms") != req.end();
if(hasSurfaceVelocityRMS) {
std::string fname = params->get<std::string>("Surface Velocity RMS File Name", "velocity_RMS.ascii");
readFileSerial(fname, tempSV, comm);
velocityRMSVec = Teuchos::rcp(new Tpetra_MultiVector (nodes_map, neq_));
velocityRMSVec->doImport(tempSV, *importOperator, Tpetra::INSERT);
}
if (comm->getRank() == 0) std::cout << " done." << std::endl;
GO elemColumnShift = (Ordering == 1) ? 1 : maxGlobalElements2D;
int lElemColumnShift = (Ordering == 1) ? 1 : cells2D.size();
int elemLayerShift = (Ordering == 0) ? 1 : numLayers;
GO vertexColumnShift = (Ordering == 1) ? 1 : maxGlobalVertices2dId;
int lVertexColumnShift = (Ordering == 1) ? 1 : nodes2D.size();
int vertexLayerShift = (Ordering == 0) ? 1 : numLayers + 1;
GO edgeColumnShift = (Ordering == 1) ? 1 : maxGlobalEdges2D;
int lEdgeColumnShift = (Ordering == 1) ? 1 : edges2D.size();
int edgeLayerShift = (Ordering == 0) ? 1 : numLayers;
this->layered_mesh_numbering = (Ordering==0) ?
Teuchos::rcp(new LayeredMeshNumbering<LO>(lVertexColumnShift,Ordering,layerThicknessRatio)):
Teuchos::rcp(new LayeredMeshNumbering<LO>(vertexLayerShift,Ordering,layerThicknessRatio));
this->SetupFieldData(comm, neq_, req, sis, worksetSize);
metaData->commit();
bulkData->modification_begin(); // Begin modifying the mesh
stk::mesh::PartVector nodePartVec;
stk::mesh::PartVector singlePartVec(1);
stk::mesh::PartVector emptyPartVec;
unsigned int ebNo = 0; //element block #???
singlePartVec[0] = nsPartVec["bottom"];
typedef AbstractSTKFieldContainer::ScalarFieldType ScalarFieldType;
typedef AbstractSTKFieldContainer::VectorFieldType VectorFieldType;
typedef AbstractSTKFieldContainer::QPScalarFieldType ElemScalarFieldType;
AbstractSTKFieldContainer::IntScalarFieldType* proc_rank_field = fieldContainer->getProcRankField();
VectorFieldType* coordinates_field = fieldContainer->getCoordinatesField();
stk::mesh::FieldBase const* coordinates_field2d = metaData2D.coordinate_field();
VectorFieldType* surface_velocity_field = metaData->get_field<VectorFieldType>(stk::topology::NODE_RANK, "surface_velocity");
VectorFieldType* surface_velocity_RMS_field = metaData->get_field<VectorFieldType>(stk::topology::NODE_RANK, "surface_velocity_rms");
ScalarFieldType* surface_height_field = metaData->get_field<ScalarFieldType>(stk::topology::NODE_RANK, "surface_height");
ScalarFieldType* thickness_field = metaData->get_field<ScalarFieldType>(stk::topology::NODE_RANK, "thickness");
ScalarFieldType* bed_topography_field = metaData->get_field<ScalarFieldType>(stk::topology::NODE_RANK, "bed_topography");
ScalarFieldType* basal_friction_field = metaData->get_field<ScalarFieldType>(stk::topology::NODE_RANK, "basal_friction");
ElemScalarFieldType* temperature_field = metaData->get_field<ElemScalarFieldType>(stk::topology::ELEMENT_RANK, "temperature");
ElemScalarFieldType* flowRate_field = metaData->get_field<ElemScalarFieldType>(stk::topology::ELEMENT_RANK, "flow_factor");
std::vector<GO> prismMpasIds(NumBaseElemeNodes), prismGlobalIds(2 * NumBaseElemeNodes);
for (int i = 0; i < (numLayers + 1) * nodes2D.size(); i++) {
int ib = (Ordering == 0) * (i % lVertexColumnShift) + (Ordering == 1) * (i / vertexLayerShift);
int il = (Ordering == 0) * (i / lVertexColumnShift) + (Ordering == 1) * (i % vertexLayerShift);
stk::mesh::Entity node;
stk::mesh::Entity node2d = nodes2D[ib];
stk::mesh::EntityId node2dId = bulkData2D.identifier(node2d) - 1;
if (il == 0)
node = bulkData->declare_entity(stk::topology::NODE_RANK, il * vertexColumnShift + vertexLayerShift * node2dId + 1, singlePartVec);
else
node = bulkData->declare_entity(stk::topology::NODE_RANK, il * vertexColumnShift + vertexLayerShift * node2dId + 1, nodePartVec);
std::vector<int> sharing_procs;
bulkData2D.comm_shared_procs( bulkData2D.entity_key(node2d), sharing_procs );
for(int iproc=0; iproc<sharing_procs.size(); ++iproc)
bulkData->add_node_sharing(node, sharing_procs[iproc]);
double* coord = stk::mesh::field_data(*coordinates_field, node);
double const* coord2d = (double const*) stk::mesh::field_data(*coordinates_field2d, node2d);
coord[0] = coord2d[0];
coord[1] = coord2d[1];
int lid = nodes_map->getLocalElement((GO)(node2dId));
coord[2] = sHeightVec_constView[lid] - thickVec_constView[lid] * (1. - levelsNormalizedThickness[il]);
if(hasSurface_height && surface_height_field) {
double* sHeight = stk::mesh::field_data(*surface_height_field, node);
sHeight[0] = sHeightVec_constView[lid];
}
if(hasThickness && thickness_field) {
double* thick = stk::mesh::field_data(*thickness_field, node);
thick[0] = thickVec_constView[lid];
}
if(hasBed_topography && bed_topography_field) {
double* bedTopo = stk::mesh::field_data(*bed_topography_field, node);
bedTopo[0] = bTopographyVec_constView[lid];
}
if(surface_velocity_field) {
double* sVelocity = stk::mesh::field_data(*surface_velocity_field, node);
Teuchos::ArrayRCP<const ST> sVelocityVec_constView_0 = sVelocityVec->getVectorNonConst(0)->get1dView();
Teuchos::ArrayRCP<const ST> sVelocityVec_constView_1 = sVelocityVec->getVectorNonConst(1)->get1dView();
sVelocity[0] = sVelocityVec_constView_0[lid];
sVelocity[1] = sVelocityVec_constView_1[lid];
}
if(surface_velocity_RMS_field) {
double* velocityRMS = stk::mesh::field_data(*surface_velocity_RMS_field, node);
Teuchos::ArrayRCP<const ST> velocityRMSVec_constView_0 = velocityRMSVec->getVectorNonConst(0)->get1dView();
Teuchos::ArrayRCP<const ST> velocityRMSVec_constView_1 = velocityRMSVec->getVectorNonConst(1)->get1dView();
velocityRMS[0] = velocityRMSVec_constView_0[lid];
velocityRMS[1] = velocityRMSVec_constView_1[lid];
}
if(hasBasal_friction && basal_friction_field) {
double* bFriction = stk::mesh::field_data(*basal_friction_field, node);
bFriction[0] = bFrictionVec->get1dView()[lid];
}
}
GO tetrasLocalIdsOnPrism[3][4];
for (int i = 0; i < cells2D.size() * numLayers; i++) {
int ib = (Ordering == 0) * (i % lElemColumnShift) + (Ordering == 1) * (i / elemLayerShift);
int il = (Ordering == 0) * (i / lElemColumnShift) + (Ordering == 1) * (i % elemLayerShift);
int shift = il * vertexColumnShift;
singlePartVec[0] = partVec[ebNo];
//TODO: this could be done only in the first layer and then copied into the other layers
stk::mesh::Entity const* rel = bulkData2D.begin_nodes(cells2D[ib]);
double tempOnPrism = 0; //Set temperature constant on each prism/Hexa
Teuchos::ArrayRCP<const ST> temperatureVecInterp_constView_il, temperatureVecInterp_constView_ilplus1;
if(hasTemperature) {
temperatureVecInterp_constView_il = temperatureVecInterp->getVectorNonConst(il)->get1dView();
temperatureVecInterp_constView_ilplus1 = temperatureVecInterp->getVectorNonConst(il + 1)->get1dView();
}
double flowRateOnPrism = 0; //Set temperature constant on each prism/Hexa
Teuchos::ArrayRCP<const ST> flowRateVecInterp_constView_il, flowRateVecInterp_constView_ilplus1;
if(hasFlowRate) {
flowRateVecInterp_constView_il = flowRateVecInterp->getVectorNonConst(il)->get1dView();
}
for (int j = 0; j < NumBaseElemeNodes; j++) {
stk::mesh::EntityId node2dId = bulkData2D.identifier(rel[j]) - 1;
int node2dLId = nodes_map->getLocalElement((GO)node2dId);
stk::mesh::EntityId mpasLowerId = vertexLayerShift * node2dId;
stk::mesh::EntityId lowerId = shift + vertexLayerShift * node2dId;
prismMpasIds[j] = mpasLowerId;
prismGlobalIds[j] = lowerId;
prismGlobalIds[j + NumBaseElemeNodes] = lowerId + vertexColumnShift;
if(hasTemperature)
tempOnPrism += 1. / NumBaseElemeNodes / 2. * (temperatureVecInterp_constView_il[node2dLId] + temperatureVecInterp_constView_ilplus1[node2dLId]);
if(hasFlowRate)
flowRateOnPrism += 1. / NumBaseElemeNodes * flowRateVecInterp_constView_il[node2dLId];
}
switch (ElemShape) {
case Tetrahedron: {
tetrasFromPrismStructured(&prismMpasIds[0], &prismGlobalIds[0], tetrasLocalIdsOnPrism);
stk::mesh::EntityId prismId = il * elemColumnShift + elemLayerShift * (bulkData2D.identifier(cells2D[ib]) - 1);
for (int iTetra = 0; iTetra < 3; iTetra++) {
stk::mesh::Entity elem = bulkData->declare_entity(stk::topology::ELEMENT_RANK, 3 * prismId + iTetra + 1, singlePartVec);
for (int j = 0; j < 4; j++) {
stk::mesh::Entity node = bulkData->get_entity(stk::topology::NODE_RANK, tetrasLocalIdsOnPrism[iTetra][j] + 1);
bulkData->declare_relation(elem, node, j);
}
int* p_rank = (int*) stk::mesh::field_data(*proc_rank_field, elem);
p_rank[0] = comm->getRank();
if(hasFlowRate && flowRate_field) {
double* flowRate = stk::mesh::field_data(*flowRate_field, elem);
flowRate[0] = flowRateOnPrism;
}
if(hasTemperature && temperature_field) {
double* temperature = stk::mesh::field_data(*temperature_field, elem);
temperature[0] = tempOnPrism;
}
}
}
break;
case Wedge:
case Hexahedron: {
stk::mesh::EntityId prismId = il * elemColumnShift + elemLayerShift * (bulkData2D.identifier(cells2D[ib]) - 1);
stk::mesh::Entity elem = bulkData->declare_entity(stk::topology::ELEMENT_RANK, prismId + 1, singlePartVec);
for (int j = 0; j < 2 * NumBaseElemeNodes; j++) {
stk::mesh::Entity node = bulkData->get_entity(stk::topology::NODE_RANK, prismGlobalIds[j] + 1);
bulkData->declare_relation(elem, node, j);
}
int* p_rank = (int*) stk::mesh::field_data(*proc_rank_field, elem);
p_rank[0] = comm->getRank();
if(hasFlowRate && flowRate_field) {
double* flowRate = stk::mesh::field_data(*flowRate_field, elem);
flowRate[0] = flowRateOnPrism;
}
if(hasTemperature && temperature_field) {
double* temperature = stk::mesh::field_data(*temperature_field, elem);
temperature[0] = tempOnPrism;
}
}
}
}
int numSubelemOnPrism, numBasalSidePoints;
int basalSideLID, upperSideLID;
switch (ElemShape) {
case Tetrahedron:
numSubelemOnPrism = 3;
numBasalSidePoints = 3;
basalSideLID = 3; //depends on how the tetrahedron is located in the Prism, see tetraFaceIdOnPrismFaceId below.
upperSideLID = 1;
break;
case Wedge:
numSubelemOnPrism = 1;
numBasalSidePoints = 3;
basalSideLID = 3; //depends on how the tetrahedron is located in the Prism.
upperSideLID = 4;
break;
case Hexahedron:
numSubelemOnPrism = 1;
numBasalSidePoints = 4;
basalSideLID = 4; //depends on how the tetrahedron is located in the Prism.
upperSideLID = 5;
break;
}
singlePartVec[0] = ssPartVec["lateralside"];
//The following two arrays have being computed offline using the computeMap function in .hpp file.
//tetraFaceIdOnPrismFaceId[ minIndex ][ PrismFaceID ]
int tetraFaceIdOnPrismFaceId[6][5] = {{0, 1, 2, 3, 1}, {2, 0, 1, 3, 1}, {1, 2, 0, 3, 1}, {2, 1, 0, 1 ,3}, {0, 2, 1, 1, 3}, {1, 0, 2, 1, 3}};
//tetraAdjacentToPrismLateralFace[ minIndex ][ prismType ][ PrismFaceID ][ iTetra ]. There are to Terahedra adjacent to a Prism face. iTetra in {0,1}
int tetraAdjacentToPrismLateralFace[6][2][3][2] = { { { { 1, 2 }, { 0, 1 }, { 0, 2 } }, { { 0, 2 }, { 0, 1 }, { 1, 2 } } },
{ { { 0, 2 }, { 1, 2 }, { 0, 1 } }, { { 1, 2 }, { 0, 2 }, { 0, 1 } } },
{ { { 0, 1 }, { 0, 2 }, { 1, 2 } }, { { 0, 1 }, { 1, 2 }, { 0, 2 } } },
{ { { 0, 2 }, { 0, 1 }, { 1, 2 } }, { { 1, 2 }, { 0, 1 }, { 0, 2 } } },
{ { { 1, 2 }, { 0, 2 }, { 0, 1 } }, { { 0, 2 }, { 1, 2 }, { 0, 1 } } },
{ { { 0, 1 }, { 1, 2 }, { 0, 2 } }, { { 0, 1 }, { 0, 2 }, { 1, 2 } } } };
for (int i = 0; i < edges2D.size() * numLayers; i++) {
int ib = (Ordering == 0) * (i % lEdgeColumnShift) + (Ordering == 1) * (i / edgeLayerShift);
// if(!isBoundaryEdge[ib]) continue; //WARNING: assuming that all the edges stored are boundary edges!!
stk::mesh::Entity edge2d = edges2D[ib];
stk::mesh::Entity const* rel = bulkData2D.begin_elements(edge2d);
stk::mesh::ConnectivityOrdinal const* ordinals = bulkData2D.begin_element_ordinals(edge2d);
int il = (Ordering == 0) * (i / lEdgeColumnShift) + (Ordering == 1) * (i % edgeLayerShift);
stk::mesh::Entity elem2d = rel[0];
stk::mesh::EntityId edgeLID = ordinals[0]; //bulkData2D.identifier(rel[0]);
stk::mesh::EntityId basalElemId = bulkData2D.identifier(elem2d) - 1;
stk::mesh::EntityId Edge2dId = bulkData2D.identifier(edge2d) - 1;
switch (ElemShape) {
case Tetrahedron: {
rel = bulkData2D.begin_nodes(elem2d);
for (int j = 0; j < NumBaseElemeNodes; j++) {
stk::mesh::EntityId node2dId = bulkData2D.identifier(rel[j]) - 1;
prismMpasIds[j] = vertexLayerShift * node2dId;
}
int minIndex;
int pType = prismType(&prismMpasIds[0], minIndex);
stk::mesh::EntityId tetraId = 3 * il * elemColumnShift + 3 * elemLayerShift * basalElemId;
stk::mesh::Entity elem0 = bulkData->get_entity(stk::topology::ELEMENT_RANK, tetraId + tetraAdjacentToPrismLateralFace[minIndex][pType][edgeLID][0] + 1);
stk::mesh::Entity elem1 = bulkData->get_entity(stk::topology::ELEMENT_RANK, tetraId + tetraAdjacentToPrismLateralFace[minIndex][pType][edgeLID][1] + 1);
stk::mesh::Entity side0 = bulkData->declare_entity(metaData->side_rank(), 2 * edgeColumnShift * il + 2 * Edge2dId * edgeLayerShift + 1, singlePartVec);
stk::mesh::Entity side1 = bulkData->declare_entity(metaData->side_rank(), 2 * edgeColumnShift * il + 2 * Edge2dId * edgeLayerShift + 1 + 1, singlePartVec);
bulkData->declare_relation(elem0, side0, tetraFaceIdOnPrismFaceId[minIndex][edgeLID]);
bulkData->declare_relation(elem1, side1, tetraFaceIdOnPrismFaceId[minIndex][edgeLID]);
stk::mesh::Entity const* rel_elemNodes0 = bulkData->begin_nodes(elem0);
stk::mesh::Entity const* rel_elemNodes1 = bulkData->begin_nodes(elem1);
for (int j = 0; j < 3; j++) {
// std::cout << j <<", " << edgeLID << ", " << minIndex << ", " << tetraFaceIdOnPrismFaceId[minIndex][edgeLID] << "," << std::endl;
stk::mesh::Entity node0 = rel_elemNodes0[this->meshSpecs[0]->ctd.side[tetraFaceIdOnPrismFaceId[minIndex][edgeLID]].node[j]];
bulkData->declare_relation(side0, node0, j);
stk::mesh::Entity node1 = rel_elemNodes1[this->meshSpecs[0]->ctd.side[tetraFaceIdOnPrismFaceId[minIndex][edgeLID]].node[j]];
bulkData->declare_relation(side1, node1, j);
}
}
break;
case Wedge:
case Hexahedron: {
stk::mesh::EntityId prismId = il * elemColumnShift + elemLayerShift * basalElemId;
stk::mesh::Entity elem = bulkData->get_entity(stk::topology::ELEMENT_RANK, prismId + 1);
stk::mesh::Entity side = bulkData->declare_entity(metaData->side_rank(), edgeColumnShift * il +Edge2dId * edgeLayerShift + 1, singlePartVec);
bulkData->declare_relation(elem, side, edgeLID);
stk::mesh::Entity const* rel_elemNodes = bulkData->begin_nodes(elem);
for (int j = 0; j < 4; j++) {
stk::mesh::Entity node = rel_elemNodes[this->meshSpecs[0]->ctd.side[edgeLID].node[j]];
bulkData->declare_relation(side, node, j);
}
}
break;
}
}
//then we store the lower and upper faces of prisms, which corresponds to triangles of the basal mesh
edgeLayerShift = (Ordering == 0) ? 1 : numLayers + 1;
edgeColumnShift = elemColumnShift;
singlePartVec[0] = ssPartVec["basalside"];
GO edgeOffset = maxGlobalEdges2D * numLayers;
if(ElemShape == Tetrahedron) edgeOffset *= 2;
for (int i = 0; i < cells2D.size(); i++) {
stk::mesh::Entity elem2d = cells2D[i];
stk::mesh::EntityId elem2d_id = bulkData2D.identifier(elem2d) - 1;
stk::mesh::Entity side = bulkData->declare_entity(metaData->side_rank(), elem2d_id + edgeOffset + 1, singlePartVec);
stk::mesh::Entity elem = bulkData->get_entity(stk::topology::ELEMENT_RANK, elem2d_id * numSubelemOnPrism * elemLayerShift + 1);
bulkData->declare_relation(elem, side, basalSideLID);
stk::mesh::Entity const* rel_elemNodes = bulkData->begin_nodes(elem);
for (int j = 0; j < numBasalSidePoints; j++) {
stk::mesh::Entity node = rel_elemNodes[this->meshSpecs[0]->ctd.side[basalSideLID].node[j]];
bulkData->declare_relation(side, node, j);
}
}
singlePartVec[0] = ssPartVec["upperside"];
edgeOffset += maxGlobalElements2D;
for (int i = 0; i < cells2D.size(); i++) {
stk::mesh::Entity elem2d = cells2D[i];
stk::mesh::EntityId elem2d_id = bulkData2D.identifier(elem2d) - 1;
stk::mesh::Entity side = bulkData->declare_entity(metaData->side_rank(), elem2d_id + edgeOffset + 1, singlePartVec);
stk::mesh::Entity elem = bulkData->get_entity(stk::topology::ELEMENT_RANK, elem2d_id * numSubelemOnPrism * elemLayerShift + (numLayers - 1) * numSubelemOnPrism * elemColumnShift + 1 + (numSubelemOnPrism - 1));
bulkData->declare_relation(elem, side, upperSideLID);
stk::mesh::Entity const* rel_elemNodes = bulkData->begin_nodes(elem);
for (int j = 0; j < numBasalSidePoints; j++) {
stk::mesh::Entity node = rel_elemNodes[this->meshSpecs[0]->ctd.side[upperSideLID].node[j]];
bulkData->declare_relation(side, node, j);
}
}
//Albany::fix_node_sharing(*bulkData);
bulkData->modification_end();
if (params->get("Export 2D Data",false))
{
// We export the basal mesh in GMSH format
std::ofstream ofile;
ofile.open (params->get("GMSH 2D Output File Name","basal_mesh.msh"));
TEUCHOS_TEST_FOR_EXCEPTION (!ofile.is_open(), std::logic_error, "Error! Cannot open file 'basal_mesh.msh'.\n");
// Preamble
ofile << "$MeshFormat\n"
<< "2.2 0 8\n"
<< "$EndMeshFormat\n";
// Nodes
ofile << "$Nodes\n" << nodes2D.size() << "\n";
stk::mesh::Entity node2d;
stk::mesh::EntityId nodeId;
for (int i(0); i<nodes2D.size(); ++i)
{
node2d = bulkData2D.get_entity(stk::topology::NODE_RANK, i + 1);
nodeId = bulkData2D.identifier(nodes2D[i]);
double const* coord2d = (double const*) stk::mesh::field_data(*coordinates_field2d, node2d);
ofile << nodeId << " " << coord2d[0] << " " << coord2d[1] << " " << 0. << "\n";
}
ofile << "$EndNodes\n";
// Mesh Elements (including edges)
ofile << "$Elements\n";
ofile << edges2D.size()+cells2D.size() << "\n";
int counter = 1;
// edges
for (int i(0); i<edges2D.size(); ++i)
{
stk::mesh::Entity const* rel = bulkData2D.begin_nodes(edges2D[i]);
ofile << counter << " " << 1 << " " << 2 << " " << 30 << " " << 1;
for (int j(0); j<2; ++j)
{
stk::mesh::EntityId node2dId = bulkData2D.identifier(rel[j]);
ofile << " " << node2dId;
}
ofile << "\n";
++counter;
}
// elements
for (int i(0); i<cells2D.size(); ++i)
{
stk::mesh::Entity const* rel = bulkData2D.begin_nodes(cells2D[i]);
ofile << counter << " " << 2 << " " << 2 << " " << 100 << " " << 11;
for (int j(0); j<3; ++j)
{
stk::mesh::EntityId node2dId = bulkData2D.identifier(rel[j]);
ofile << " " << node2dId;
}
ofile << "\n";
++counter;
}
ofile << "$EndElements\n";
ofile.close();
}
}
Albany::OrdinarySTKFieldContainer<Interleaved>::OrdinarySTKFieldContainer(
const Teuchos::RCP<Teuchos::ParameterList>& params_,
const Teuchos::RCP<stk::mesh::MetaData>& metaData_,
const int neq_,
const AbstractFieldContainer::FieldContainerRequirements& req,
const int numDim_,
const Teuchos::RCP<Albany::StateInfoStruct>& sis)
: GenericSTKFieldContainer<Interleaved>(params_, metaData_, neq_, numDim_),
buildSphereVolume(false) {
typedef typename AbstractSTKFieldContainer::VectorFieldType VFT;
typedef typename AbstractSTKFieldContainer::ScalarFieldType SFT;
#ifdef ALBANY_LCM
buildSphereVolume = (std::find(req.begin(), req.end(), "Sphere Volume") != req.end());
#endif
//Start STK stuff
this->coordinates_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, "coordinates");
solution_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK,
params_->get<std::string>("Exodus Solution Name", "solution"));
#ifdef ALBANY_LCM
residual_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK,
params_->get<std::string>("Exodus Residual Name", "residual"));
#endif
stk::mesh::put_field(*this->coordinates_field , metaData_->universal_part(), numDim_);
stk::mesh::put_field(*solution_field , metaData_->universal_part(), neq_);
#ifdef ALBANY_LCM
stk::mesh::put_field(*residual_field , metaData_->universal_part() , neq_);
#endif
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*this->coordinates_field, Ioss::Field::MESH);
stk::io::set_field_role(*solution_field, Ioss::Field::TRANSIENT);
#ifdef ALBANY_LCM
stk::io::set_field_role(*residual_field, Ioss::Field::TRANSIENT);
#endif
#endif
#ifdef ALBANY_LCM
// sphere volume is a mesh attribute read from a genesis mesh file containing sphere element (used for peridynamics)
if(buildSphereVolume){
this->sphereVolume_field = metaData_->get_field< stk::mesh::Field<double> >(stk::topology::ELEMENT_RANK, "volume");
TEUCHOS_TEST_FOR_EXCEPTION(this->sphereVolume_field == 0, std::logic_error, "\n**** Error: Expected volume field for sphere elements, field not found.\n");
stk::io::set_field_role(*this->sphereVolume_field, Ioss::Field::ATTRIBUTE);
}
#endif
// If the problem requests that the initial guess at the solution equals the input node coordinates,
// set that here
/*
if(std::find(req.begin(), req.end(), "Initial Guess Coords") != req.end()){
this->copySTKField(this->coordinates_field, solution_field);
}
*/
this->buildStateStructs(sis);
initializeSTKAdaptation();
}
Albany::OrdinarySTKFieldContainer<Interleaved>::OrdinarySTKFieldContainer(
const Teuchos::RCP<Teuchos::ParameterList>& params_,
const Teuchos::RCP<stk::mesh::MetaData>& metaData_,
const int neq_,
const AbstractFieldContainer::FieldContainerRequirements& req,
const int numDim_,
const Teuchos::RCP<Albany::StateInfoStruct>& sis)
: GenericSTKFieldContainer<Interleaved>(params_, metaData_, neq_, numDim_),
buildSphereVolume(false) {
typedef typename AbstractSTKFieldContainer::VectorFieldType VFT;
typedef typename AbstractSTKFieldContainer::ScalarFieldType SFT;
//Start STK stuff
this->coordinates_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, "coordinates");
solution_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK,
params_->get<std::string>("Exodus Solution Name", "solution"));
#if defined(ALBANY_LCM)
residual_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK,
params_->get<std::string>("Exodus Residual Name", "residual"));
#endif
stk::mesh::put_field(*this->coordinates_field , metaData_->universal_part(), numDim_);
stk::mesh::put_field(*solution_field , metaData_->universal_part(), neq_);
#if defined(ALBANY_LCM)
stk::mesh::put_field(*residual_field , metaData_->universal_part() , neq_);
#endif
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*this->coordinates_field, Ioss::Field::MESH);
stk::io::set_field_role(*solution_field, Ioss::Field::TRANSIENT);
#if defined(ALBANY_LCM)
stk::io::set_field_role(*residual_field, Ioss::Field::TRANSIENT);
#endif
#endif
#if defined(ALBANY_LCM)
// sphere volume is a mesh attribute read from a genesis mesh file containing sphere element (used for peridynamics)
// for whatever reason, its type is stk::mesh::Field<double, stk::mesh::Cartesian3d>
// the read won't work if you try to read it as a SFT
bool hasSphereVolumeFieldContainerRequirement = (std::find(req.begin(), req.end(), "Sphere Volume") != req.end());
if(hasSphereVolumeFieldContainerRequirement){
this->sphereVolume_field = metaData_->template get_field< stk::mesh::Field<double, stk::mesh::Cartesian3d> >(stk::topology::ELEMENT_RANK, "volume");
if(this->sphereVolume_field != 0){
buildSphereVolume = true;
stk::io::set_field_role(*this->sphereVolume_field, Ioss::Field::ATTRIBUTE);
}
}
#endif
// If the problem requests that the initial guess at the solution equals the input node coordinates,
// set that here
/*
if(std::find(req.begin(), req.end(), "Initial Guess Coords") != req.end()){
this->copySTKField(this->coordinates_field, solution_field);
}
*/
this->buildStateStructs(sis);
initializeSTKAdaptation();
}
void
Albany::IossSTKMeshStruct::setFieldAndBulkData (
const Teuchos::RCP<const Teuchos_Comm>& commT,
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(commT, neq_, req, sis, worksetSize);
mesh_data->set_bulk_data(*bulkData);
*out << "IOSS-STK: number of node sets = " << nsPartVec.size() << std::endl;
*out << "IOSS-STK: number of side sets = " << ssPartVec.size() << std::endl;
mesh_data->add_all_mesh_fields_as_input_fields();
std::vector<stk::io::MeshField> missing;
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->get_input_io_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){
// trick to avoid hanging
bulkData->modification_begin();
if(commT->getRank() == 0){ // read in the mesh on PE 0
//stk::io::process_mesh_bulk_data(region, *bulkData);
mesh_data->populate_bulk_data();
//bulkData = &mesh_data->bulk_data();
// 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;
mesh_data->read_defined_input_fields(index, &missing);
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;
mesh_data->read_defined_input_fields(res_time, &missing);
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;
}
}
else {
// trick to avoid hanging
bulkData->modification_begin(); bulkData->modification_begin();
}
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
mesh_data->populate_bulk_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;
mesh_data->read_defined_input_fields(index, &missing);
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;
mesh_data->read_defined_input_fields(res_time, &missing);
m_restartDataTime = res_time;
m_hasRestartSolution = true;
}
else
{
*out << "Neither restart index or time are set. We still read defined fields in case they are needed (e.g., parameters)."<< std::endl;
// *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;
}
}
}
#ifdef ALBANY_FELIX
// Load required fields
stk::mesh::Selector select_owned_in_part = stk::mesh::Selector(metaData->universal_part()) & stk::mesh::Selector(metaData->locally_owned_part());
stk::mesh::Selector select_overlap_in_part = stk::mesh::Selector(metaData->universal_part()) & (stk::mesh::Selector(metaData->locally_owned_part()) | stk::mesh::Selector(metaData->globally_shared_part()));
std::vector<stk::mesh::Entity> nodes;
stk::mesh::get_selected_entities(select_overlap_in_part, bulkData->buckets(stk::topology::NODE_RANK), nodes);
std::vector<stk::mesh::Entity> elems;
stk::mesh::get_selected_entities(select_owned_in_part, bulkData->buckets(stk::topology::ELEM_RANK), elems);
GO numOwnedNodes(0);
GO numOwnedElems(0);
numOwnedNodes = stk::mesh::count_selected_entities(select_owned_in_part, bulkData->buckets(stk::topology::NODE_RANK));
numOwnedElems = stk::mesh::count_selected_entities(select_owned_in_part, bulkData->buckets(stk::topology::ELEM_RANK));
GO numGlobalVertices = 0;
GO numGlobalElements = 0;
Teuchos::reduceAll<int, GO>(*commT, Teuchos::REDUCE_SUM, 1, &numOwnedNodes, &numGlobalVertices);
Teuchos::reduceAll<int, GO>(*commT, Teuchos::REDUCE_SUM, 1, &numOwnedElems, &numGlobalElements);
if (commT->getRank() == 0)
{
*out << "Checking if requirements are already stored in the mesh. If not, we import them from ascii files.\n";
}
Teuchos::Array<GO> nodeIndices(nodes.size()), elemIndices(elems.size());
for (int i = 0; i < nodes.size(); ++i)
nodeIndices[i] = bulkData->identifier(nodes[i]) - 1;
for (int i = 0; i < elems.size(); ++i)
elemIndices[i] = bulkData->identifier(elems[i]) - 1;
// Creating the serial and parallel node maps
const Tpetra::global_size_t INVALID = Teuchos::OrdinalTraits<Tpetra::global_size_t>::invalid ();
Teuchos::RCP<const Tpetra_Map> nodes_map = Tpetra::createNonContigMapWithNode<LO, GO> (nodeIndices, commT, KokkosClassic::Details::getNode<KokkosNode>());
Teuchos::RCP<const Tpetra_Map> elems_map = Tpetra::createNonContigMapWithNode<LO, GO> (elemIndices, commT, KokkosClassic::Details::getNode<KokkosNode>());
int numMyNodes = (commT->getRank() == 0) ? numGlobalVertices : 0;
int numMyElements = (commT->getRank() == 0) ? numGlobalElements : 0;
Teuchos::RCP<const Tpetra_Map> serial_nodes_map = Teuchos::rcp(new const Tpetra_Map(INVALID, numMyNodes, 0, commT));
Teuchos::RCP<const Tpetra_Map> serial_elems_map = Teuchos::rcp(new const Tpetra_Map(INVALID, numMyElements, 0, commT));
// Creating the Tpetra_Import object (to transfer from serial to parallel vectors)
Tpetra_Import importOperatorNode (serial_nodes_map, nodes_map);
Tpetra_Import importOperatorElem (serial_elems_map, elems_map);
Teuchos::ParameterList* req_fields_info;
if (params->isSublist("Required Fields Info"))
{
req_fields_info = ¶ms->sublist("Required Fields Info");
for (AbstractFieldContainer::FieldContainerRequirements::const_iterator it=req.begin(); it!=req.end(); ++it)
{
// Get the file name
std::string temp_str = *it + " File Name";
std::string fname = req_fields_info->get<std::string>(temp_str,"");
// Ge the file type (if not specified, assume Scalar)
temp_str = *it + " Field Type";
std::string ftype = req_fields_info->get<std::string>(temp_str,"");
if (ftype=="")
{
*out << "Warning! No field type specified for field " << *it << ". We skip it and hope is already present in the mesh...\n";
continue;
}
stk::mesh::Entity node, elem;
stk::mesh::EntityId nodeId, elemId;
int lid;
double* values;
typedef AbstractSTKFieldContainer::QPScalarFieldType QPScalarFieldType;
typedef AbstractSTKFieldContainer::QPVectorFieldType QPVectorFieldType;
typedef AbstractSTKFieldContainer::ScalarFieldType ScalarFieldType;
typedef AbstractSTKFieldContainer::VectorFieldType VectorFieldType;
// Depending on the field type, we need to use different pointers
if (ftype == "Node Scalar")
{
// Creating the serial and (possibly) parallel Tpetra service vectors
Tpetra_Vector serial_req_vec(serial_nodes_map);
Tpetra_Vector req_vec(nodes_map);
temp_str = *it + " Value";
if (req_fields_info->isParameter(temp_str))
{
*out << "Discarding other info about Node Scalar field " << *it << " and filling it with constant value " << req_fields_info->get<double>(temp_str) << "\n";
// For debug, we allow to fill the field with a given uniform value
fillTpetraVec (serial_req_vec,req_fields_info->get<double>(temp_str));
}
else if (fname!="")
{
*out << "Reading Node Scalar field " << *it << " from file " << fname << "\n";
// Read the input file and stuff it in the Tpetra vector
readScalarFileSerial (fname,serial_req_vec,commT);
temp_str = *it + " Scale Factor";
if (req_fields_info->isParameter(temp_str))
{
double scale_factor = req_fields_info->get<double>(temp_str);
serial_req_vec.scale (scale_factor);
}
}
else
{
bool found = false;
for (int i(0); i<missing.size(); ++i)
{
if (missing[i].field()->name()==*it)
{
*out << "No file name nor constant value specified for Node Scalar field " << *it << "; initializing it to 0.\n";
fillTpetraVec (serial_req_vec,0.);
found = true;
break;
}
}
if (!found)
{
*out << "Using mesh-stored values for Node Scalar field " << *it << " since no constant value nor filename has been specified\n";
continue;
}
}
// Fill the (possibly) parallel vector
req_vec.doImport(serial_req_vec,importOperatorNode,Tpetra::INSERT);
// Extracting the mesh field and the tpetra vector view
ScalarFieldType* field = metaData->get_field<ScalarFieldType>(stk::topology::NODE_RANK, *it);
TEUCHOS_TEST_FOR_EXCEPTION (field==0, std::logic_error, "Error! Field " << *it << " not present (perhaps is 'Elem Scalar'?).\n");
Teuchos::ArrayRCP<const ST> req_vec_view = req_vec.get1dView();
//Now we have to stuff the vector in the mesh data
for (int i(0); i<nodes.size(); ++i)
{
nodeId = bulkData->identifier(nodes[i]) - 1;
lid = nodes_map->getLocalElement((GO)(nodeId));
values = stk::mesh::field_data(*field, nodes[i]);
values[0] = req_vec_view[lid];
}
}
else if (ftype == "Elem Scalar")
{
// Creating the serial and (possibly) parallel Tpetra service vectors
Tpetra_Vector serial_req_vec(serial_elems_map);
Tpetra_Vector req_vec(elems_map);
temp_str = *it + " Value";
if (req_fields_info->isParameter(temp_str))
{
*out << "Discarding other info about Elem Scalar field " << *it << " and filling it with constant value " << req_fields_info->get<double>(temp_str) << "\n";
// For debug, we allow to fill the field with a given uniform value
fillTpetraVec (serial_req_vec,req_fields_info->get<double>(temp_str));
}
else if (fname!="")
{
*out << "Reading Elem Scalar field " << *it << " from file " << fname << "\n";
// Read the input file and stuff it in the Tpetra vector
readScalarFileSerial (fname,serial_req_vec,commT);
temp_str = *it + " Scale Factor";
if (req_fields_info->isParameter(temp_str))
{
double scale_factor = req_fields_info->get<double>(temp_str);
serial_req_vec.scale (scale_factor);
}
}
else
{
bool found = false;
for (int i(0); i<missing.size(); ++i)
{
if (missing[i].field()->name()==*it)
{
*out << "No file name nor constant value specified for Elem Scalar field " << *it << "; initializing it to 0.\n";
fillTpetraVec (serial_req_vec,0.);
found = true;
break;
}
}
if (!found)
{
*out << "Using mesh-stored values for Elem Scalar field " << *it << " since no constant value nor filename has been specified\n";
continue;
}
}
// Fill the (possibly) parallel vector
req_vec.doImport(serial_req_vec,importOperatorElem,Tpetra::INSERT);
// Extracting the mesh field and the tpetra vector view
QPScalarFieldType* field = metaData->get_field<QPScalarFieldType>(stk::topology::ELEM_RANK, *it);
TEUCHOS_TEST_FOR_EXCEPTION (field==0, std::logic_error, "Error! Field " << *it << " not present (perhaps is 'Node Scalar'?).\n");
Teuchos::ArrayRCP<const ST> req_vec_view = req_vec.get1dView();
//Now we have to stuff the vector in the mesh data
for (int i(0); i<elems.size(); ++i)
{
elemId = bulkData->identifier(elems[i]) - 1;
lid = elems_map->getLocalElement((GO)(elemId));
values = stk::mesh::field_data(*field, elems[i]);
values[0] = req_vec_view[lid];
}
}
else if (ftype == "Node Vector")
{
// Loading the dimension of the Vector Field (by default equal to the mesh dimension)
temp_str = *it + " Field Dimension";
int fieldDim = req_fields_info->get<int>(temp_str,this->meshSpecs[0]->numDim);
// Creating the serial and (possibly) parallel Tpetra service multivectors
Tpetra_MultiVector serial_req_mvec(serial_nodes_map,fieldDim);
Tpetra_MultiVector req_mvec(nodes_map,fieldDim);
temp_str = *it + " Value";
if (req_fields_info->isParameter(temp_str))
{
*out << "Discarding other info about Node Vector field " << *it << " and filling it with constant value "
<< req_fields_info->get<Teuchos::Array<double> >(temp_str) << "\n";
// For debug, we allow to fill the field with a given uniform value
fillTpetraMVec (serial_req_mvec,req_fields_info->get<Teuchos::Array<double> >(temp_str));
}
else if (fname!="")
{
*out << "Reading Node Vector field " << *it << " from file " << fname << "\n";
// Read the input file and stuff it in the Tpetra multivector
readVectorFileSerial (fname,serial_req_mvec,commT);
temp_str = *it + " Scale Factor";
if (req_fields_info->isParameter(temp_str))
{
double scale_factor = req_fields_info->get<double>(temp_str);
serial_req_mvec.scale (scale_factor);
}
}
else
{
bool found = false;
for (int i(0); i<missing.size(); ++i)
{
if (missing[i].field()->name()==*it)
{
*out << "No file name nor constant value specified for Node Vector field " << *it << "; initializing it to 0.\n";
Teuchos::Array<double> vals(fieldDim,0.);
fillTpetraMVec (serial_req_mvec,vals);
found = true;
break;
}
}
if (!found)
{
*out << "Using mesh-stored values for Node Vector field " << *it << " since no constant value nor filename has been specified\n";
continue;
}
}
// Fill the (possibly) parallel vector
req_mvec.doImport(serial_req_mvec,importOperatorNode,Tpetra::INSERT);
// Extracting the mesh field and the tpetra vector views
VectorFieldType* field = metaData->get_field<VectorFieldType>(stk::topology::NODE_RANK, *it);
TEUCHOS_TEST_FOR_EXCEPTION (field==0, std::logic_error, "Error! Field " << *it << " not present (perhaps is 'Elem Vector'?).\n");
std::vector<Teuchos::ArrayRCP<const ST> > req_mvec_view;
for (int i(0); i<fieldDim; ++i)
req_mvec_view.push_back(req_mvec.getVector(i)->get1dView());
//Now we have to stuff the vector in the mesh data
for (int i(0); i<nodes.size(); ++i)
{
nodeId = bulkData->identifier(nodes[i]) - 1;
lid = nodes_map->getLocalElement((GO)(nodeId));
values = stk::mesh::field_data(*field, nodes[i]);
for (int iDim(0); iDim<fieldDim; ++iDim)
values[iDim] = req_mvec_view[iDim][lid];
}
}
else if (ftype == "Elem Vector")
{
// Loading the dimension of the Vector Field (by default equal to the mesh dimension)
temp_str = *it + " Field Dimension";
int fieldDim = req_fields_info->get<int>(temp_str,this->meshSpecs[0]->numDim);
// Creating the serial and (possibly) parallel Tpetra service multivectors
Tpetra_MultiVector serial_req_mvec(serial_elems_map,fieldDim);
Tpetra_MultiVector req_mvec(elems_map,fieldDim);
temp_str = *it + " Value";
if (req_fields_info->isParameter(temp_str))
{
*out << "Discarding other info about Elem Vector field " << *it << " and filling it with constant value "
<< req_fields_info->get<Teuchos::Array<double> >(temp_str) << "\n";
// For debug, we allow to fill the field with a given uniform value
fillTpetraMVec (serial_req_mvec,req_fields_info->get<Teuchos::Array<double> >(temp_str));
}
else if (fname!="")
{
*out << "Reading Elem Vector field " << *it << " from file " << fname << "\n";
// Read the input file and stuff it in the Tpetra multivector
readVectorFileSerial (fname,serial_req_mvec,commT);
temp_str = *it + " Scale Factor";
if (req_fields_info->isParameter(temp_str))
{
double scale_factor = req_fields_info->get<double>(temp_str);
serial_req_mvec.scale (scale_factor);
}
}
else
{
bool found = false;
for (int i(0); i<missing.size(); ++i)
{
if (missing[i].field()->name()==*it)
{
*out << "No file name nor constant value specified for Elem Vector field " << *it << "; initializing it to 0.\n";
Teuchos::Array<double> vals(fieldDim,0.);
fillTpetraMVec (serial_req_mvec,vals);
found = true;
break;
}
}
if (!found)
{
*out << "Using mesh-stored values for Elem Vector field " << *it << " since no constant value nor filename has been specified\n";
continue;
}
}
// Fill the (possibly) parallel vector
req_mvec.doImport(serial_req_mvec,importOperatorElem,Tpetra::INSERT);
// Extracting the mesh field and the tpetra vector views
VectorFieldType* field = metaData->get_field<VectorFieldType>(stk::topology::ELEM_RANK, *it);
TEUCHOS_TEST_FOR_EXCEPTION (field==0, std::logic_error, "Error! Field " << *it << " not present (perhaps is 'Node Vector'?).\n");
std::vector<Teuchos::ArrayRCP<const ST> > req_mvec_view;
for (int i(0); i<fieldDim; ++i)
req_mvec_view.push_back(req_mvec.getVector(i)->get1dView());
//Now we have to stuff the vector in the mesh data
for (int i(0); i<elems.size(); ++i)
{
elemId = bulkData->identifier(elems[i]) - 1;
lid = elems_map->getLocalElement((GO)(elemId));
values = stk::mesh::field_data(*field, nodes[i]);
for (int iDim(0); iDim<fieldDim; ++iDim)
values[iDim] = req_mvec_view[iDim][lid];
}
}
else
{
TEUCHOS_TEST_FOR_EXCEPTION (true, Teuchos::Exceptions::InvalidParameterValue,
"Sorry, I haven't yet implemented the case of field that are not Scalar nor Vector or that is not at nodal nor elemental.\n");
}
}
}
if (params->get<bool>("Write points coordinates to ascii file", false))
{
AbstractSTKFieldContainer::VectorFieldType* coordinates_field = fieldContainer->getCoordinatesField();
std::ofstream ofile;
ofile.open("coordinates.ascii");
if (!ofile.is_open())
{
TEUCHOS_TEST_FOR_EXCEPTION (true, std::logic_error, "Error! Cannot open coordinates file.\n");
}
ofile << nodes.size() << " " << 4 << "\n";
stk::mesh::Entity node;
for (int i(0); i<nodes.size(); ++i)
{
node = bulkData->get_entity(stk::topology::NODE_RANK, i + 1);
double* coord = stk::mesh::field_data(*coordinates_field, node);
ofile << bulkData->identifier (nodes[i]) << " " << coord[0] << " " << coord[1] << " " << coord[2] << "\n";
}
ofile.close();
}
#endif
// Refine the mesh before starting the simulation if indicated
uniformRefineMesh(commT);
// Rebalance the mesh before starting the simulation if indicated
rebalanceInitialMeshT(commT);
// Build additional mesh connectivity needed for mesh fracture (if indicated)
computeAddlConnectivity();
}
Albany::OrdinarySTKFieldContainer<Interleaved>::OrdinarySTKFieldContainer(
const Teuchos::RCP<Teuchos::ParameterList>& params_,
stk::mesh::fem::FEMMetaData* metaData_,
stk::mesh::BulkData* bulkData_,
const int neq_,
const AbstractFieldContainer::FieldContainerRequirements& req,
const int numDim_,
const Teuchos::RCP<Albany::StateInfoStruct>& sis)
: GenericSTKFieldContainer<Interleaved>(params_, metaData_, bulkData_, neq_, numDim_),
buildSurfaceHeight(false),
buildTemperature(false),
buildBasalFriction(false),
buildThickness(false),
buildFlowFactor(false),
buildSurfaceVelocity(false),
buildVelocityRMS(false) {
typedef typename AbstractSTKFieldContainer::VectorFieldType VFT;
typedef typename AbstractSTKFieldContainer::ScalarFieldType SFT;
#ifdef ALBANY_FELIX
buildSurfaceHeight = (std::find(req.begin(), req.end(), "Surface Height") != req.end());
buildTemperature = (std::find(req.begin(), req.end(), "Temperature") != req.end());
buildBasalFriction = (std::find(req.begin(), req.end(), "Basal Friction") != req.end());
buildThickness = (std::find(req.begin(), req.end(), "Thickness") != req.end());
buildFlowFactor = (std::find(req.begin(), req.end(), "Flow Factor") != req.end());
buildSurfaceVelocity = (std::find(req.begin(), req.end(), "Surface Velocity") != req.end());
buildVelocityRMS = (std::find(req.begin(), req.end(), "Velocity RMS") != req.end());
#endif
//Start STK stuff
this->coordinates_field = & metaData_->declare_field< VFT >("coordinates");
solution_field = & metaData_->declare_field< VFT >(
params_->get<std::string>("Exodus Solution Name", "solution"));
#ifdef ALBANY_LCM
residual_field = & metaData_->declare_field< VFT >(
params_->get<std::string>("Exodus Residual Name", "residual"));
#endif
#ifdef ALBANY_FELIX
if(buildSurfaceHeight)
this->surfaceHeight_field = & metaData_->declare_field< SFT >("surface_height");
if(buildTemperature)
this->temperature_field = & metaData_->declare_field< SFT >("temperature");
if(buildBasalFriction)
this->basalFriction_field = & metaData_->declare_field< SFT >("basal_friction");
if(buildThickness)
this->thickness_field = & metaData_->declare_field< SFT >("thickness");
if(buildFlowFactor)
this->flowFactor_field = & metaData_->declare_field< SFT >("flow_factor");
if(buildSurfaceVelocity)
this->surfaceVelocity_field = & metaData_->declare_field< VFT >("surface_velocity");
if(buildVelocityRMS)
this->velocityRMS_field = & metaData_->declare_field< VFT >("velocity_RMS");
#endif
stk::mesh::put_field(*this->coordinates_field , metaData_->node_rank() , metaData_->universal_part(), numDim_);
stk::mesh::put_field(*solution_field , metaData_->node_rank() , metaData_->universal_part(), neq_);
#ifdef ALBANY_LCM
stk::mesh::put_field(*residual_field , metaData_->node_rank() , metaData_->universal_part() , neq_);
#endif
#ifdef ALBANY_FELIX
if(buildSurfaceHeight)
stk::mesh::put_field( *this->surfaceHeight_field , metaData_->node_rank() , metaData_->universal_part());
if(buildTemperature)
stk::mesh::put_field( *this->temperature_field , metaData_->element_rank() , metaData_->universal_part());
if(buildBasalFriction)
stk::mesh::put_field( *this->basalFriction_field , metaData_->node_rank() , metaData_->universal_part());//*metaData_->get_part("basalside","Mpas Interface"));
if(buildThickness)
stk::mesh::put_field( *this->thickness_field , metaData_->node_rank() , metaData_->universal_part());
if(buildFlowFactor)
stk::mesh::put_field( *this->flowFactor_field , metaData_->element_rank() , metaData_->universal_part());
if(buildSurfaceVelocity)
stk::mesh::put_field( *this->surfaceVelocity_field , metaData_->node_rank() , metaData_->universal_part(), neq_);
if(buildVelocityRMS)
stk::mesh::put_field( *this->velocityRMS_field , metaData_->node_rank() , metaData_->universal_part(), neq_);
#endif
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*this->coordinates_field, Ioss::Field::MESH);
stk::io::set_field_role(*solution_field, Ioss::Field::TRANSIENT);
#ifdef ALBANY_LCM
stk::io::set_field_role(*residual_field, Ioss::Field::TRANSIENT);
#endif
#ifdef ALBANY_FELIX
// ATTRIBUTE writes only once per file, but somehow did not work on restart.
//stk::io::set_field_role(*surfaceHeight_field, Ioss::Field::ATTRIBUTE);
if(buildSurfaceHeight)
stk::io::set_field_role(*this->surfaceHeight_field, Ioss::Field::TRANSIENT);
if(buildTemperature)
stk::io::set_field_role(*this->temperature_field, Ioss::Field::TRANSIENT);
if(buildBasalFriction)
stk::io::set_field_role(*this->basalFriction_field, Ioss::Field::TRANSIENT);
if(buildThickness)
stk::io::set_field_role(*this->thickness_field, Ioss::Field::TRANSIENT);
if(buildFlowFactor)
stk::io::set_field_role(*this->flowFactor_field, Ioss::Field::TRANSIENT);
if(buildSurfaceVelocity)
stk::io::set_field_role(*this->surfaceVelocity_field, Ioss::Field::TRANSIENT);
if(buildVelocityRMS)
stk::io::set_field_role(*this->velocityRMS_field, Ioss::Field::TRANSIENT);
#endif
#endif
// If the problem requests that the initial guess at the solution equals the input node coordinates,
// set that here
/*
if(std::find(req.begin(), req.end(), "Initial Guess Coords") != req.end()){
this->copySTKField(this->coordinates_field, solution_field);
}
*/
this->buildStateStructs(sis);
initializeSTKAdaptation();
}
Albany::MultiSTKFieldContainer<Interleaved>::MultiSTKFieldContainer(
const Teuchos::RCP<Teuchos::ParameterList>& params_,
const Teuchos::RCP<stk::mesh::MetaData>& metaData_,
const Teuchos::RCP<stk::mesh::BulkData>& bulkData_,
const int neq_,
const AbstractFieldContainer::FieldContainerRequirements& req,
const int numDim_,
const Teuchos::RCP<Albany::StateInfoStruct>& sis,
const Teuchos::Array<Teuchos::Array<std::string> >& solution_vector,
const Teuchos::Array<std::string>& residual_vector)
: GenericSTKFieldContainer<Interleaved>(params_, metaData_, bulkData_, neq_, numDim_),
haveResidual(false), buildSphereVolume(false) {
typedef typename AbstractSTKFieldContainer::VectorFieldType VFT;
typedef typename AbstractSTKFieldContainer::ScalarFieldType SFT;
typedef typename AbstractSTKFieldContainer::SphereVolumeFieldType SVFT;
sol_vector_name.resize(solution_vector.size());
sol_index.resize(solution_vector.size());
// Check the input
for(int vec_num = 0; vec_num < solution_vector.size(); vec_num++){
if(solution_vector[vec_num].size() == 0) { // Do the default solution vector
std::string name = params_->get<std::string>(sol_tag_name[vec_num], sol_id_name[vec_num]);
VFT* solution = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, name);
stk::mesh::put_field(*solution, metaData_->universal_part(), neq_);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*solution, Ioss::Field::TRANSIENT);
#endif
sol_vector_name[vec_num].push_back(name);
sol_index[vec_num].push_back(this->neq);
}
else if(solution_vector[vec_num].size() == 1) { // User is just renaming the entire solution vector
VFT* solution = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, solution_vector[vec_num][0]);
stk::mesh::put_field(*solution, metaData_->universal_part(), neq_);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*solution, Ioss::Field::TRANSIENT);
#endif
sol_vector_name[vec_num].push_back(solution_vector[vec_num][0]);
sol_index[vec_num].push_back(neq_);
}
else { // user is breaking up the solution into multiple fields
// make sure the number of entries is even
TEUCHOS_TEST_FOR_EXCEPTION((solution_vector[vec_num].size() % 2), std::logic_error,
"Error in input file: specification of solution vector layout is incorrect." << std::endl);
int len, accum = 0;
for(int i = 0; i < solution_vector[vec_num].size(); i += 2) {
if(solution_vector[vec_num][i + 1] == "V") {
len = numDim_; // vector
accum += len;
VFT* solution = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, solution_vector[vec_num][i]);
stk::mesh::put_field(*solution, metaData_->universal_part(), len);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*solution, Ioss::Field::TRANSIENT);
#endif
sol_vector_name[vec_num].push_back(solution_vector[vec_num][i]);
sol_index[vec_num].push_back(len);
}
else if(solution_vector[vec_num][i + 1] == "S") {
len = 1; // scalar
accum += len;
SFT* solution = & metaData_->declare_field< SFT >(stk::topology::NODE_RANK, solution_vector[vec_num][i]);
stk::mesh::put_field(*solution, metaData_->universal_part());
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*solution, Ioss::Field::TRANSIENT);
#endif
sol_vector_name[vec_num].push_back(solution_vector[vec_num][i]);
sol_index[vec_num].push_back(len);
}
else
TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error,
"Error in input file: specification of solution vector layout is incorrect." << std::endl);
}
TEUCHOS_TEST_FOR_EXCEPTION(accum != neq_, std::logic_error,
"Error in input file: specification of solution vector layout is incorrect." << std::endl);
}
}
#if defined(ALBANY_LCM)
// do the residual next
if(residual_vector.size() == 0) { // Do the default residual vector
std::string name = params_->get<std::string>(res_tag_name, res_id_name);
VFT* residual = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, name);
stk::mesh::put_field(*residual, metaData_->universal_part(), neq_);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*residual, Ioss::Field::TRANSIENT);
#endif
res_vector_name.push_back(name);
res_index.push_back(neq_);
}
else if(residual_vector.size() == 1) { // User is just renaming the entire residual vector
VFT* residual = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, residual_vector[0]);
stk::mesh::put_field(*residual, metaData_->universal_part(), neq_);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*residual, Ioss::Field::TRANSIENT);
#endif
res_vector_name.push_back(residual_vector[0]);
res_index.push_back(neq_);
}
else { // user is breaking up the residual into multiple fields
// make sure the number of entries is even
TEUCHOS_TEST_FOR_EXCEPTION((residual_vector.size() % 2), std::logic_error,
"Error in input file: specification of residual vector layout is incorrect." << std::endl);
int len, accum = 0;
for(int i = 0; i < residual_vector.size(); i += 2) {
if(residual_vector[i + 1] == "V") {
len = numDim_; // vector
accum += len;
VFT* residual = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, residual_vector[i]);
stk::mesh::put_field(*residual, metaData_->universal_part(), len);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*residual, Ioss::Field::TRANSIENT);
#endif
res_vector_name.push_back(residual_vector[i]);
res_index.push_back(len);
}
else if(residual_vector[i + 1] == "S") {
len = 1; // scalar
accum += len;
SFT* residual = & metaData_->declare_field< SFT >(stk::topology::NODE_RANK, residual_vector[i]);
stk::mesh::put_field(*residual, metaData_->universal_part());
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*residual, Ioss::Field::TRANSIENT);
#endif
res_vector_name.push_back(residual_vector[i]);
res_index.push_back(len);
}
else
TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error,
"Error in input file: specification of residual vector layout is incorrect." << std::endl);
}
TEUCHOS_TEST_FOR_EXCEPTION(accum != neq_, std::logic_error,
"Error in input file: specification of residual vector layout is incorrect." << std::endl);
}
haveResidual = true;
#endif
//Do the coordinates
this->coordinates_field = & metaData_->declare_field< VFT >(stk::topology::NODE_RANK, "coordinates");
stk::mesh::put_field(*this->coordinates_field , metaData_->universal_part(), numDim_);
#ifdef ALBANY_SEACAS
stk::io::set_field_role(*this->coordinates_field, Ioss::Field::MESH);
#endif
#if defined(ALBANY_LCM) && defined(ALBANY_SEACAS)
// sphere volume is a mesh attribute read from a genesis mesh file containing sphere element (used for peridynamics)
bool hasSphereVolumeFieldContainerRequirement = (std::find(req.begin(), req.end(), "Sphere Volume") != req.end());
if(hasSphereVolumeFieldContainerRequirement){
this->sphereVolume_field = metaData_->template get_field< SVFT >(stk::topology::ELEMENT_RANK, "volume");
if(this->sphereVolume_field != 0){
buildSphereVolume = true;
stk::io::set_field_role(*this->sphereVolume_field, Ioss::Field::ATTRIBUTE);
}
}
#endif
this->addStateStructs(sis);
initializeSTKAdaptation();
}
