//Wedge
Albany::MpasSTKMeshStruct::MpasSTKMeshStruct(const Teuchos::RCP<Teuchos::ParameterList>& params,
const Teuchos::RCP<const Epetra_Comm>& comm,
const std::vector<int>& indexToTriangleID, const std::vector<int>& verticesOnTria, int nGlobalTriangles, int numLayers, int Ordering) :
GenericSTKMeshStruct(params,Teuchos::null,3),
out(Teuchos::VerboseObjectBase::getDefaultOStream()),
periodic(false),
NumEles(indexToTriangleID.size()),
hasRestartSol(false),
restartTime(0.)
{
std::vector<int> indexToPrismID(indexToTriangleID.size()*numLayers);
//Int ElemColumnShift = (ordering == ColumnWise) ? 1 : indexToTriangleID.size();
int elemColumnShift = (Ordering == 1) ? 1 : nGlobalTriangles;
int lElemColumnShift = (Ordering == 1) ? 1 : indexToTriangleID.size();
int elemLayerShift = (Ordering == 0) ? 1 : numLayers;
for(int il=0; il< numLayers; il++)
{
int shift = il*elemColumnShift;
int lShift = il*lElemColumnShift;
for(int j=0; j< indexToTriangleID.size(); j++)
{
int lid = lShift + j*elemLayerShift;
indexToPrismID[lid] = shift+elemLayerShift * indexToTriangleID[j];
}
}
elem_map = Teuchos::rcp(new Epetra_Map(nGlobalTriangles*numLayers, indexToPrismID.size(), &indexToPrismID[0], 0, *comm)); // Distribute the elems equally
params->validateParameters(*getValidDiscretizationParameters(),0);
std::string ebn="Element Block 0";
partVec[0] = & metaData->declare_part(ebn, stk::topology::ELEMENT_RANK );
ebNameToIndex[ebn] = 0;
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*partVec[0]);
#endif
std::vector<std::string> nsNames;
std::string nsn="Lateral";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, stk::topology::NODE_RANK );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="Internal";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, stk::topology::NODE_RANK );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="Bottom";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, stk::topology::NODE_RANK );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
std::vector<std::string> ssNames;
std::string ssnLat="lateralside";
std::string ssnBottom="basalside";
std::string ssnTop="upperside";
ssNames.push_back(ssnLat);
ssNames.push_back(ssnBottom);
ssNames.push_back(ssnTop);
ssPartVec[ssnLat] = & metaData->declare_part(ssnLat, metaData->side_rank() );
ssPartVec[ssnBottom] = & metaData->declare_part(ssnBottom, metaData->side_rank() );
ssPartVec[ssnTop] = & metaData->declare_part(ssnTop, metaData->side_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*ssPartVec[ssnLat]);
stk::io::put_io_part_attribute(*ssPartVec[ssnBottom]);
stk::io::put_io_part_attribute(*ssPartVec[ssnTop]);
#endif
stk::mesh::set_cell_topology<shards::Wedge<6> >(*partVec[0]);
stk::mesh::set_cell_topology<shards::Triangle<3> >(*ssPartVec[ssnBottom]);
stk::mesh::set_cell_topology<shards::Triangle<3> >(*ssPartVec[ssnTop]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnLat]);
numDim = 3;
int cub = params->get("Cubature Degree",3);
int worksetSizeMax = params->get("Workset Size",50);
int worksetSize = this->computeWorksetSize(worksetSizeMax, elem_map->NumMyElements());
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(),
ebNameToIndex, this->interleavedOrdering));
}
Albany::ExtrudedSTKMeshStruct::ExtrudedSTKMeshStruct(const Teuchos::RCP<Teuchos::ParameterList>& params, const Teuchos::RCP<const Teuchos_Comm>& comm) :
GenericSTKMeshStruct(params, Teuchos::null, 3), out(Teuchos::VerboseObjectBase::getDefaultOStream()), periodic(false) {
params->validateParameters(*getValidDiscretizationParameters(), 0);
std::string ebn = "Element Block 0";
partVec[0] = &metaData->declare_part(ebn, stk::topology::ELEMENT_RANK);
ebNameToIndex[ebn] = 0;
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*partVec[0]);
#endif
std::vector<std::string> nsNames;
std::string nsn = "lateral";
nsNames.push_back(nsn);
nsPartVec[nsn] = &metaData->declare_part(nsn, stk::topology::NODE_RANK);
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn = "internal";
nsNames.push_back(nsn);
nsPartVec[nsn] = &metaData->declare_part(nsn, stk::topology::NODE_RANK);
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn = "bottom";
nsNames.push_back(nsn);
nsPartVec[nsn] = &metaData->declare_part(nsn, stk::topology::NODE_RANK);
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
std::vector<std::string> ssNames;
std::string ssnLat = "lateralside";
std::string ssnBottom = "basalside";
std::string ssnTop = "upperside";
ssNames.push_back(ssnLat);
ssNames.push_back(ssnBottom);
ssNames.push_back(ssnTop);
ssPartVec[ssnLat] = &metaData->declare_part(ssnLat, metaData->side_rank());
ssPartVec[ssnBottom] = &metaData->declare_part(ssnBottom, metaData->side_rank());
ssPartVec[ssnTop] = &metaData->declare_part(ssnTop, metaData->side_rank());
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*ssPartVec[ssnLat]);
stk::io::put_io_part_attribute(*ssPartVec[ssnBottom]);
stk::io::put_io_part_attribute(*ssPartVec[ssnTop]);
#endif
Teuchos::RCP<Teuchos::ParameterList> params2D(new Teuchos::ParameterList());
params2D->set("Use Serial Mesh", params->get("Use Serial Mesh", false));
params2D->set<int>("Number Of Time Derivatives", params->get<int>("Number Of Time Derivatives"));
#ifdef ALBANY_SEACAS
params2D->set("Exodus Input File Name", params->get("Exodus Input File Name", "IceSheet.exo"));
basalMeshStruct = Teuchos::rcp(new Albany::IossSTKMeshStruct(params2D, adaptParams, comm));
#else
// Above block of code could allow for 2D mesh to come from other sources instead of Ioss
TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error,
std::endl << "Error in ExtrudedSTKMeshStruct: Currently Requires 2D mesh to come from exodus");
#endif
Teuchos::RCP<Albany::StateInfoStruct> sis = Teuchos::rcp(new Albany::StateInfoStruct);
Albany::AbstractFieldContainer::FieldContainerRequirements req;
int ws_size = basalMeshStruct->getMeshSpecs()[0]->worksetSize;
basalMeshStruct->setFieldAndBulkData(comm, params, 1, req, sis, ws_size);
stk::mesh::Selector select_owned_in_part = stk::mesh::Selector(basalMeshStruct->metaData->universal_part()) & stk::mesh::Selector(basalMeshStruct->metaData->locally_owned_part());
int numCells = stk::mesh::count_selected_entities(select_owned_in_part, basalMeshStruct->bulkData->buckets(stk::topology::ELEMENT_RANK));
std::string shape = params->get("Element Shape", "Hexahedron");
std::string basalside_name;
if(shape == "Tetrahedron") {
ElemShape = Tetrahedron;
basalside_name = shards::getCellTopologyData<shards::Triangle<3> >()->name;
}
else if (shape == "Wedge") {
ElemShape = Wedge;
basalside_name = shards::getCellTopologyData<shards::Triangle<3> >()->name;
}
else if (shape == "Hexahedron") {
ElemShape = Hexahedron;
basalside_name = shards::getCellTopologyData<shards::Quadrilateral<4> >()->name;
}
else
TEUCHOS_TEST_FOR_EXCEPTION(true, Teuchos::Exceptions::InvalidParameterValue,
std::endl << "Error in ExtrudedSTKMeshStruct: Element Shape " << shape << " not recognized. Possible values: Tetrahedron, Wedge, Hexahedron");
std::string elem2d_name(basalMeshStruct->getMeshSpecs()[0]->ctd.base->name);
TEUCHOS_TEST_FOR_EXCEPTION(basalside_name != elem2d_name, Teuchos::Exceptions::InvalidParameterValue,
std::endl << "Error in ExtrudedSTKMeshStruct: Expecting topology name of elements of 2d mesh to be " << basalside_name << " but it is " << elem2d_name);
switch (ElemShape) {
case Tetrahedron:
stk::mesh::set_cell_topology<shards::Tetrahedron<4> >(*partVec[0]);
stk::mesh::set_cell_topology<shards::Triangle<3> >(*ssPartVec[ssnBottom]);
stk::mesh::set_cell_topology<shards::Triangle<3> >(*ssPartVec[ssnTop]);
stk::mesh::set_cell_topology<shards::Triangle<3> >(*ssPartVec[ssnLat]);
NumBaseElemeNodes = 3;
break;
case Wedge:
stk::mesh::set_cell_topology<shards::Wedge<6> >(*partVec[0]);
stk::mesh::set_cell_topology<shards::Triangle<3> >(*ssPartVec[ssnBottom]);
stk::mesh::set_cell_topology<shards::Triangle<3> >(*ssPartVec[ssnTop]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnLat]);
NumBaseElemeNodes = 3;
break;
case Hexahedron:
stk::mesh::set_cell_topology<shards::Hexahedron<8> >(*partVec[0]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnBottom]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnTop]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnLat]);
NumBaseElemeNodes = 4;
break;
}
numDim = 3;
int cub = params->get("Cubature Degree", 3);
int worksetSizeMax = params->get("Workset Size", 50);
int worksetSize = this->computeWorksetSize(worksetSizeMax, numCells);
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(), ebNameToIndex, this->interleavedOrdering));
}
Albany::MpasSTKMeshStruct::MpasSTKMeshStruct(const Teuchos::RCP<Teuchos::ParameterList>& params,
const Teuchos::RCP<const Epetra_Comm>& comm,
const std::vector<int>& indexToTriangleID, const std::vector<int>& verticesOnTria, int nGlobalTriangles) :
GenericSTKMeshStruct(params,Teuchos::null, 2),
out(Teuchos::VerboseObjectBase::getDefaultOStream()),
periodic(false),
NumEles(indexToTriangleID.size()),
hasRestartSol(false),
restartTime(0.)
{
elem_map = Teuchos::rcp(new Epetra_Map(nGlobalTriangles, indexToTriangleID.size(), &indexToTriangleID[0], 0, *comm)); // Distribute the elems equally
params->validateParameters(*getValidDiscretizationParameters(),0);
std::string ebn="Element Block 0";
partVec[0] = & metaData->declare_part(ebn, stk::topology::ELEMENT_RANK );
ebNameToIndex[ebn] = 0;
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*partVec[0]);
#endif
std::vector<std::string> nsNames;
std::string nsn="Lateral";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, stk::topology::NODE_RANK );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="Internal";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, stk::topology::NODE_RANK );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
std::vector<std::string> ssNames;
std::string ssn="LateralSide";
ssNames.push_back(ssn);
ssPartVec[ssn] = & metaData->declare_part(ssn, metaData->side_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*ssPartVec[ssn]);
#endif
stk::mesh::set_cell_topology<shards::Triangle<3> >(*partVec[0]);
stk::mesh::set_cell_topology<shards::Line<2> >(*ssPartVec[ssn]);
numDim = 2;
int cub = params->get("Cubature Degree",3);
int worksetSizeMax = params->get("Workset Size",50);
int worksetSize = this->computeWorksetSize(worksetSizeMax, elem_map->NumMyElements());
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(),
ebNameToIndex, this->interleavedOrdering));
}
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::AsciiSTKMeshStruct::AsciiSTKMeshStruct(
const Teuchos::RCP<Teuchos::ParameterList>& params,
const Teuchos::RCP<const Epetra_Comm>& comm) :
GenericSTKMeshStruct(params,Teuchos::null,3),
out(Teuchos::VerboseObjectBase::getDefaultOStream()),
periodic(false)
{
int numProc = comm->NumProc(); //total number of processors
contigIDs = params->get("Contiguous IDs", true);
std::cout << "Number of processors: " << numProc << std::endl;
//names of files giving the mesh
char meshfilename[100];
char shfilename[100];
char confilename[100];
char bffilename[100];
char geIDsfilename[100];
char gnIDsfilename[100];
char bfIDsfilename[100];
char flwafilename[100]; //flow factor file
char tempfilename[100]; //temperature file
char betafilename[100]; //basal friction coefficient file
if ((numProc == 1) & (contigIDs == true)) { //serial run with contiguous global IDs
std::cout << "Ascii mesh has contiguous IDs; no bfIDs, geIDs, gnIDs files required." << std::endl;
sprintf(meshfilename, "%s", "xyz");
sprintf(shfilename, "%s", "sh");
sprintf(confilename, "%s", "eles");
sprintf(bffilename, "%s", "bf");
sprintf(flwafilename, "%s", "flwa");
sprintf(tempfilename, "%s", "temp");
sprintf(betafilename, "%s", "beta");
}
else { //parallel run or serial run with non-contiguous global IDs - proc # is appended to file name to indicate what processor the mesh piece is on
if ((numProc == 1) & (contigIDs == false))
std::cout << "1 processor run with non-contiguous IDs; bfIDs0, geIDs0, gnIDs0 files required." << std::endl;
int suffix = comm->MyPID(); //current processor number
sprintf(meshfilename, "%s%i", "xyz", suffix);
sprintf(shfilename, "%s%i", "sh", suffix);
sprintf(confilename, "%s%i", "eles", suffix);
sprintf(bffilename, "%s%i", "bf", suffix);
sprintf(geIDsfilename, "%s%i", "geIDs", suffix);
sprintf(gnIDsfilename, "%s%i", "gnIDs", suffix);
sprintf(bfIDsfilename, "%s%i", "bfIDs", suffix);
sprintf(flwafilename, "%s%i", "flwa", suffix);
sprintf(tempfilename, "%s%i", "temp", suffix);
sprintf(betafilename, "%s%i", "beta", suffix);
}
//read in coordinates of mesh -- right now hard coded for 3D
//assumes mesh file is called "xyz" and its first row is the number of nodes
FILE *meshfile = fopen(meshfilename,"r");
if (meshfile == NULL) { //check if coordinates file exists
*out << "Error in AsciiSTKMeshStruct: coordinates file " << meshfilename <<" not found!"<< std::endl;
TEUCHOS_TEST_FOR_EXCEPTION(true, Teuchos::Exceptions::InvalidParameter,
std::endl << "Error in AsciiSTKMeshStruct: coordinates file " << meshfilename << " not found!"<< std::endl);
}
double temp;
fseek(meshfile, 0, SEEK_SET);
fscanf(meshfile, "%lf", &temp);
NumNodes = int(temp);
std::cout << "numNodes: " << NumNodes << std::endl;
xyz = new double[NumNodes][3];
char buffer[100];
fgets(buffer, 100, meshfile);
for (int i=0; i<NumNodes; i++){
fgets(buffer, 100, meshfile);
sscanf(buffer, "%lf %lf %lf", &xyz[i][0], &xyz[i][1], &xyz[i][2]);
//*out << "i: " << i << ", x: " << xyz[i][0] << ", y: " << xyz[i][1] << ", z: " << xyz[i][2] << std::endl;
}
//read in surface height data from mesh
//assumes surface height file is called "sh" and its first row is the number of nodes
FILE *shfile = fopen(shfilename,"r");
have_sh = false;
if (shfile != NULL) have_sh = true;
if (have_sh) {
fseek(shfile, 0, SEEK_SET);
fscanf(shfile, "%lf", &temp);
int NumNodesSh = int(temp);
std::cout << "NumNodesSh: " << NumNodesSh<< std::endl;
if (NumNodesSh != NumNodes) {
*out << "Error in AsciiSTKMeshStruct: sh file must have same number nodes as xyz file! numNodes in xyz = " << NumNodes <<", numNodes in sh = "<< NumNodesSh << std::endl;
TEUCHOS_TEST_FOR_EXCEPTION(true, Teuchos::Exceptions::InvalidParameter,
std::endl << "Error in AsciiSTKMeshStruct: sh file must have same number nodes as xyz file! numNodes in xyz = " << NumNodes << ", numNodes in sh = "<< NumNodesSh << std::endl);
}
sh = new double[NumNodes];
fgets(buffer, 100, shfile);
for (int i=0; i<NumNodes; i++){
fgets(buffer, 100, shfile);
sscanf(buffer, "%lf", &sh[i]);
//*out << "i: " << i << ", sh: " << sh[i] << std::endl;
}
}
//read in connectivity file -- right now hard coded for 3D hexes
//assumes mesh file is called "eles" and its first row is the number of elements
FILE *confile = fopen(confilename,"r");
if (confile == NULL) { //check if element connectivity file exists
*out << "Error in AsciiSTKMeshStruct: element connectivity file " << confilename <<" not found!"<< std::endl;
TEUCHOS_TEST_FOR_EXCEPTION(true, Teuchos::Exceptions::InvalidParameter,
std::endl << "Error in AsciiSTKMeshStruct: element connectivity file " << confilename << " not found!"<< std::endl);
}
fseek(confile, 0, SEEK_SET);
fscanf(confile, "%lf", &temp);
NumEles = int(temp);
std::cout << "numEles: " << NumEles << std::endl;
eles = new int[NumEles][8];
fgets(buffer, 100, confile);
for (int i=0; i<NumEles; i++){
fgets(buffer, 100, confile);
sscanf(buffer, "%i %i %i %i %i %i %i %i", &eles[i][0], &eles[i][1], &eles[i][2], &eles[i][3], &eles[i][4], &eles[i][5], &eles[i][6], &eles[i][7]);
//*out << "elt # " << i << ": " << eles[i][0] << " " << eles[i][1] << " " << eles[i][2] << " " << eles[i][3] << " " << eles[i][4] << " "
// << eles[i][5] << " " << eles[i][6] << " " << eles[i][7] << std::endl;
}
//read in basal face connectivity file from ascii file
//assumes basal face connectivity file is called "bf" and its first row is the number of faces on basal boundary
FILE *bffile = fopen(bffilename,"r");
have_bf = false;
if (bffile != NULL) have_bf = true;
if (have_bf) {
fseek(bffile, 0, SEEK_SET);
fscanf(bffile, "%lf", &temp);
NumBasalFaces = int(temp);
std::cout << "numBasalFaces: " << NumBasalFaces << std::endl;
bf = new int[NumBasalFaces][5]; //1st column of bf: element # that face belongs to, 2rd-5th columns of bf: connectivity (hard-coded for quad faces)
fgets(buffer, 100, bffile);
for (int i=0; i<NumBasalFaces; i++){
fgets(buffer, 100, bffile);
sscanf(buffer, "%i %i %i %i %i", &bf[i][0], &bf[i][1], &bf[i][2], &bf[i][3], &bf[i][4]);
//*out << "face #:" << bf[i][0] << ", face conn:" << bf[i][1] << " " << bf[i][2] << " " << bf[i][3] << " " << bf[i][4] << std::endl;
}
}
//Create array w/ global element IDs
globalElesID = new int[NumEles];
if ((numProc == 1) & (contigIDs == true)) { //serial run with contiguous global IDs: element IDs are just 0->NumEles-1
for (int i=0; i<NumEles; i++) {
globalElesID[i] = i;
//*out << "local element ID #:" << i << ", global element ID #:" << globalElesID[i] << std::endl;
}
}
else {//parallel run: read global element IDs from file.
//This file should have a header like the other files, and length NumEles.
FILE *geIDsfile = fopen(geIDsfilename,"r");
if (geIDsfile == NULL) { //check if global element IDs file exists
*out << "Error in AsciiSTKMeshStruct: global element IDs file " << geIDsfilename <<" not found!"<< std::endl;
TEUCHOS_TEST_FOR_EXCEPTION(true, Teuchos::Exceptions::InvalidParameter,
std::endl << "Error in AsciiSTKMeshStruct: global element IDs file " << geIDsfilename << " not found!"<< std::endl);
}
fseek(geIDsfile, 0, SEEK_SET);
fgets(buffer, 100, geIDsfile);
for (int i=0; i<NumEles; i++){
fgets(buffer, 100, geIDsfile);
sscanf(buffer, "%i ", &globalElesID[i]);
globalElesID[i] = globalElesID[i]-1; //subtract 1 b/c global element IDs file assumed to be 1-based not 0-based
//*out << "local element ID #:" << i << ", global element ID #:" << globalElesID[i] << std::endl;
}
}
//Create array w/ global node IDs
globalNodesID = new int[NumNodes];
if ((numProc == 1) & (contigIDs == true)) { //serial run with contiguous global IDs: element IDs are just 0->NumEles-1
for (int i=0; i<NumNodes; i++) {
globalNodesID[i] = i;
//*out << "local node ID #:" << i << ", global node ID #:" << globalNodesID[i] << std::endl;
}
}
else {//parallel run: read global node IDs from file.
//This file should have a header like the other files, and length NumNodes
FILE *gnIDsfile = fopen(gnIDsfilename,"r");
if (gnIDsfile == NULL) { //check if global node IDs file exists
*out << "Error in AsciiSTKMeshStruct: global node IDs file " << gnIDsfilename <<" not found!"<< std::endl;
TEUCHOS_TEST_FOR_EXCEPTION(true, Teuchos::Exceptions::InvalidParameter,
std::endl << "Error in AsciiSTKMeshStruct: global node IDs file " << gnIDsfilename << " not found!"<< std::endl);
}
fseek(gnIDsfile, 0, SEEK_SET);
fgets(buffer, 100, gnIDsfile);
for (int i=0; i<NumNodes; i++){
fgets(buffer, 100, gnIDsfile);
sscanf(buffer, "%i ", &globalNodesID[i]);
globalNodesID[i] = globalNodesID[i]-1; //subtract 1 b/c global node IDs file assumed to be 1-based not 0-based
//*out << "local node ID #:" << i << ", global node ID #:" << globalNodesID[i] << std::endl;
}
}
basalFacesID = new int[NumBasalFaces];
if ((numProc == 1) & (contigIDs == true)) { //serial run with contiguous global IDs: element IDs are just 0->NumEles-1
for (int i=0; i<NumBasalFaces; i++) {
basalFacesID[i] = i;
//*out << "local face ID #:" << i << ", global face ID #:" << basalFacesID[i] << std::endl;
}
}
else {//parallel run: read basal face IDs from file.
//This file should have a header like the other files, and length NumBasalFaces
FILE *bfIDsfile = fopen(bfIDsfilename,"r");
fseek(bfIDsfile, 0, SEEK_SET);
fgets(buffer, 100, bfIDsfile);
for (int i=0; i<NumBasalFaces; i++){
fgets(buffer, 100, bfIDsfile);
sscanf(buffer, "%i ", &basalFacesID[i]);
basalFacesID[i] = basalFacesID[i]-1; //subtract 1 b/c basal face IDs file assumed to be 1-based not 0-based
//*out << "local face ID #:" << i << ", global face ID #:" << basalFacesID[i] << std::endl;
}
}
//read in flow factor (flwa) data from mesh
//assumes flow factor file is called "flwa" and its first row is the number of elements in the mesh
FILE *flwafile = fopen(flwafilename,"r");
have_flwa = false;
if (flwafile != NULL) have_flwa = true;
if (have_flwa) {
fseek(flwafile, 0, SEEK_SET);
fscanf(flwafile, "%lf", &temp);
flwa = new double[NumEles];
fgets(buffer, 100, flwafile);
for (int i=0; i<NumEles; i++){
fgets(buffer, 100, flwafile);
sscanf(buffer, "%lf", &flwa[i]);
//*out << "i: " << i << ", flwa: " << flwa[i] << std::endl;
}
}
//read in temperature data from mesh
//assumes temperature file is called "temp" and its first row is the number of elements in the mesh
FILE *tempfile = fopen(tempfilename,"r");
have_temp = false;
if (tempfile != NULL) have_temp = true;
if (have_temp) {
fseek(tempfile, 0, SEEK_SET);
fscanf(tempfile, "%lf", &temp);
temper = new double[NumEles];
fgets(buffer, 100, tempfile);
for (int i=0; i<NumEles; i++){
fgets(buffer, 100, tempfile);
sscanf(buffer, "%lf", &temper[i]);
//*out << "i: " << i << ", temp: " << temper[i] << std::endl;
}
}
//read in basal friction (beta) data from mesh
//assumes basal friction file is called "beta" and its first row is the number of nodes
FILE *betafile = fopen(betafilename,"r");
have_beta = false;
if (betafile != NULL) have_beta = true;
if (have_beta) {
fseek(betafile, 0, SEEK_SET);
fscanf(betafile, "%lf", &temp);
beta = new double[NumNodes];
fgets(buffer, 100, betafile);
for (int i=0; i<NumNodes; i++){
fgets(buffer, 100, betafile);
sscanf(buffer, "%lf", &beta[i]);
//*out << "i: " << i << ", beta: " << beta[i] << std::endl;
}
}
elem_map = Teuchos::rcp(new Epetra_Map(-1, NumEles, globalElesID, 0, *comm)); //Distribute the elements according to the global element IDs
node_map = Teuchos::rcp(new Epetra_Map(-1, NumNodes, globalNodesID, 0, *comm)); //Distribute the nodes according to the global node IDs
basal_face_map = Teuchos::rcp(new Epetra_Map(-1, NumBasalFaces, basalFacesID, 0, *comm)); //Distribute the elements according to the basal face IDs
params->validateParameters(*getValidDiscretizationParameters(),0);
std::string ebn="Element Block 0";
partVec[0] = & metaData->declare_part(ebn, metaData->element_rank() );
ebNameToIndex[ebn] = 0;
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*partVec[0]);
#endif
std::vector<std::string> nsNames;
std::string nsn="Bottom";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, metaData->node_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="NodeSet0";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, metaData->node_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="NodeSet1";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, metaData->node_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="NodeSet2";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, metaData->node_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="NodeSet3";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, metaData->node_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="NodeSet4";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, metaData->node_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
nsn="NodeSet5";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, metaData->node_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
std::vector<std::string> ssNames;
std::string ssn="Basal";
ssNames.push_back(ssn);
ssPartVec[ssn] = & metaData->declare_part(ssn, metaData->side_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*ssPartVec[ssn]);
#endif
stk::mesh::fem::set_cell_topology<shards::Hexahedron<8> >(*partVec[0]);
stk::mesh::fem::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssn]);
numDim = 3;
int cub = params->get("Cubature Degree",3);
int worksetSizeMax = params->get("Workset Size",50);
int worksetSize = this->computeWorksetSize(worksetSizeMax, elem_map->NumMyElements());
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(),
ebNameToIndex, this->interleavedOrdering));
}
//Constructor for arrays passed from CISM through Albany-CISM interface
Albany::CismSTKMeshStruct::CismSTKMeshStruct(
const Teuchos::RCP<Teuchos::ParameterList>& params,
const Teuchos::RCP<const Teuchos_Comm>& commT,
const double * xyz_at_nodes_Ptr,
const int * global_node_id_owned_map_Ptr,
const int * global_element_id_active_owned_map_Ptr,
const int * global_element_conn_active_Ptr,
const int * global_basal_face_active_owned_map_Ptr,
const int * global_top_face_active_owned_map_Ptr,
const int * global_basal_face_conn_active_Ptr,
const int * global_top_face_conn_active_Ptr,
const int * global_west_face_active_owned_map_Ptr,
const int * global_west_face_conn_active_Ptr,
const int * global_east_face_active_owned_map_Ptr,
const int * global_east_face_conn_active_Ptr,
const int * global_south_face_active_owned_map_Ptr,
const int * global_south_face_conn_active_Ptr,
const int * global_north_face_active_owned_map_Ptr,
const int * global_north_face_conn_active_Ptr,
const int * dirichlet_node_mask_Ptr,
const double * uvel_at_nodes_Ptr,
const double * vvel_at_nodes_Ptr,
const double * beta_at_nodes_Ptr,
const double * surf_height_at_nodes_Ptr,
const double * dsurf_height_at_nodes_dx_Ptr,
const double * dsurf_height_at_nodes_dy_Ptr,
const double * thick_at_nodes_Ptr,
const double * flwa_at_active_elements_Ptr,
const int nNodes, const int nElementsActive,
const int nCellsActive, const int nWestFacesActive,
const int nEastFacesActive, const int nSouthFacesActive,
const int nNorthFacesActive,
const int verbosity) :
GenericSTKMeshStruct(params,Teuchos::null,3),
out(Teuchos::VerboseObjectBase::getDefaultOStream()),
hasRestartSol(false),
restartTime(0.0),
periodic(false)
{
if (verbosity == 1 & commT->getRank() == 0) std::cout <<"In Albany::CismSTKMeshStruct - double * array inputs!" << std::endl;
NumNodes = nNodes;
NumEles = nElementsActive;
NumBasalFaces = nCellsActive;
NumWestFaces = nWestFacesActive;
NumEastFaces = nEastFacesActive;
NumSouthFaces = nSouthFacesActive;
NumNorthFaces = nNorthFacesActive;
debug_output_verbosity = verbosity;
if (verbosity == 2) {
std::cout <<"Proc #" << commT->getRank() << ", NumNodes = " << NumNodes << ", NumEles = "<< NumEles << ", NumBasalFaces = " << NumBasalFaces
<<", NumWestFaces = " << NumWestFaces << ", NumEastFaces = "<< NumEastFaces
<< ", NumSouthFaces = " << NumSouthFaces << ", NumNorthFaces = " << NumNorthFaces << std::endl;
}
xyz = new double[NumNodes][3];
eles = new int[NumEles][8];
dirichletNodeMask = new int[NumNodes];
//1st column of bf: element # that face belongs to, 2rd-5th columns of bf: connectivity (hard-coded for quad faces)
bf = new int[NumBasalFaces][5];
tf = new int[NumBasalFaces][5];
wf = new int[NumWestFaces][5];
ef = new int[NumEastFaces][5];
sf = new int[NumSouthFaces][5];
nf = new int[NumNorthFaces][5];
sh = new double[NumNodes];
thck = new double[NumNodes];
shGrad = new double[NumNodes][2];
globalNodesID = new GO[NumNodes];
globalElesID = new GO[NumEles];
basalFacesID = new GO[NumBasalFaces];
topFacesID = new GO[NumBasalFaces];
westFacesID = new GO[NumWestFaces];
eastFacesID = new GO[NumEastFaces];
southFacesID = new GO[NumSouthFaces];
northFacesID = new GO[NumNorthFaces];
flwa = new double[NumEles];
beta = new double[NumNodes];
uvel = new double[NumNodes];
vvel = new double[NumNodes];
//TO DO? pass in temper? for now, flwa is passed instead of temper
//temper = new double[NumEles];
//check if optional input fields exist
if (surf_height_at_nodes_Ptr != NULL) have_sh = true;
else have_sh = false;
if (thick_at_nodes_Ptr != NULL) have_thck = true;
else have_thck = false;
if (dsurf_height_at_nodes_dx_Ptr != NULL && dsurf_height_at_nodes_dy_Ptr != NULL) have_shGrad = true;
else have_shGrad = false;
if (global_basal_face_active_owned_map_Ptr != NULL) have_bf = true;
else have_bf = false;
if (global_top_face_active_owned_map_Ptr != NULL) have_tf = true;
else have_tf = false;
if (flwa_at_active_elements_Ptr != NULL) have_flwa = true;
else have_flwa = false;
if (beta_at_nodes_Ptr != NULL) have_beta = true;
else have_beta = false;
if (global_west_face_active_owned_map_Ptr != NULL && NumWestFaces > 0) have_wf = true;
else have_wf = false;
if (global_east_face_active_owned_map_Ptr != NULL && NumEastFaces > 0) have_ef = true;
else have_ef = false;
if (global_south_face_active_owned_map_Ptr != NULL && NumSouthFaces > 0) have_sf = true;
else have_sf = false;
if (global_north_face_active_owned_map_Ptr != NULL && NumNorthFaces > 0) have_nf = true;
else have_nf = false;
have_temp = false; //for now temperature field is not passed; flwa is passed instead
if (dirichlet_node_mask_Ptr != NULL) have_dirichlet = true;
else have_dirichlet = false;
for (int i=0; i<NumNodes; i++){
globalNodesID[i] = global_node_id_owned_map_Ptr[i]-1;
for (int j=0; j<3; j++)
xyz[i][j] = xyz_at_nodes_Ptr[i + NumNodes*j];
//*out << "i: " << i << ", x: " << xyz[i][0]
//<< ", y: " << xyz[i][1] << ", z: " << xyz[i][2] << std::endl;
}
if (have_sh) {
for (int i=0; i<NumNodes; i++)
sh[i] = surf_height_at_nodes_Ptr[i];
}
if (have_thck) {
for (int i=0; i<NumNodes; i++)
thck[i] = thick_at_nodes_Ptr[i];
}
if (have_shGrad) {
for (int i=0; i<NumNodes; i++){
shGrad[i][0] = dsurf_height_at_nodes_dx_Ptr[i];
shGrad[i][1] = dsurf_height_at_nodes_dy_Ptr[i];
}
}
if (have_beta) {
for (int i=0; i<NumNodes; i++) {
beta[i] = beta_at_nodes_Ptr[i];
//*out << "beta[i] " << beta[i] << std::endl;
}
}
for (int i=0; i<NumEles; i++) {
globalElesID[i] = global_element_id_active_owned_map_Ptr[i]-1;
for (int j = 0; j<8; j++)
eles[i][j] = global_element_conn_active_Ptr[i + nElementsActive*j];
//*out << "elt # " << globalElesID[i] << ": " << eles[i][0]
// << " " << eles[i][1] << " " << eles[i][2] << " "
// << eles[i][3] << " " << eles[i][4] << " "
// << eles[i][5] << " " << eles[i][6] << " " << eles[i][7] << std::endl;
}
if (have_dirichlet) {
for (int i=0; i<NumNodes; i++) {
dirichletNodeMask[i] = dirichlet_node_mask_Ptr[i];
uvel[i] = uvel_at_nodes_Ptr[i];
vvel[i] = vvel_at_nodes_Ptr[i];
//*out << "i: " << i << ", x: " << xyz[i][0]
// << ", y: " << xyz[i][1] << ", z: " << xyz[i][2] << ", dirichlet: " << dirichletNodeMask[i] << std::endl;
/*if (abs(uvel[i]) > 0) {
*out << "i: " << i << ", x: " << xyz[i][0]
<< ", y: " << xyz[i][1] << ", z: " << xyz[i][2] << ", uvel: " << uvel[i] << ", vvel: " << vvel[i] << std::endl;
}*/
}
}
if (have_flwa) {
for (int i=0; i<NumEles; i++)
flwa[i] = flwa_at_active_elements_Ptr[i];
}
if (have_bf) {
for (int i=0; i<NumBasalFaces; i++) {
basalFacesID[i] = global_basal_face_active_owned_map_Ptr[i]-1;
for (int j=0; j<5; j++)
bf[i][j] = global_basal_face_conn_active_Ptr[i + nCellsActive*j];
//*out << "bf # " << basalFacesID[i] << ": " << bf[i][0] << " " << bf[i][1] << " " << bf[i][2] << " " << bf[i][3] << " " << bf[i][4] << std::endl;
}
}
if (have_tf) {
for (int i=0; i<NumBasalFaces; i++) {
topFacesID[i] = global_top_face_active_owned_map_Ptr[i]-1;
for (int j=0; j<5; j++)
tf[i][j] = global_top_face_conn_active_Ptr[i + nCellsActive*j];
}
}
if (have_wf) {
for (int i=0; i<NumWestFaces; i++) {
westFacesID[i] = global_west_face_active_owned_map_Ptr[i]-1;
for (int j=0; j<5; j++)
wf[i][j] = global_west_face_conn_active_Ptr[i + NumWestFaces*j];
}
}
if (have_ef) {
for (int i=0; i<NumEastFaces; i++) {
eastFacesID[i] = global_east_face_active_owned_map_Ptr[i]-1;
for (int j=0; j<5; j++)
ef[i][j] = global_east_face_conn_active_Ptr[i + NumEastFaces*j];
}
}
if (have_sf) {
for (int i=0; i<NumSouthFaces; i++) {
southFacesID[i] = global_south_face_active_owned_map_Ptr[i]-1;
for (int j=0; j<5; j++)
sf[i][j] = global_south_face_conn_active_Ptr[i + NumSouthFaces*j];
/*if (commT->getRank() == 0) {
*out << "proc 0, sf # " << southFacesID[i] << ": " << sf[i][0] << " " << sf[i][1] << " " << sf[i][2] << " " << sf[i][3] << " " << sf[i][4] << std::endl; }
if (commT->getRank() == 1) {
*out << "proc 1, sf # " << southFacesID[i] << ": " << sf[i][0] << " " << sf[i][1] << " " << sf[i][2] << " " << sf[i][3] << " " << bf[i][4] << std::endl; }
if (commT->getRank() == 2) {
*out << "proc 2, sf # " << southFacesID[i] << ": " << sf[i][0] << " " << sf[i][1] << " " << sf[i][2] << " " << sf[i][3] << " " << sf[i][4] << std::endl; }
if (commT->getRank() == 3) {
*out << "proc 3, sf # " << southFacesID[i] << ": " << sf[i][0] << " " << sf[i][1] << " " << sf[i][2] << " " << sf[i][3] << " " << sf[i][4] << std::endl; } */
}
}
if (have_nf) {
for (int i=0; i<NumNorthFaces; i++) {
northFacesID[i] = global_north_face_active_owned_map_Ptr[i]-1;
for (int j=0; j<5; j++)
nf[i][j] = global_north_face_conn_active_Ptr[i + NumNorthFaces*j];
}
}
Teuchos::ArrayView<const GO> globalElesIDAV = Teuchos::arrayView(globalElesID, NumEles);
Teuchos::ArrayView<const GO> globalNodesIDAV = Teuchos::arrayView(globalNodesID, NumNodes);
Teuchos::ArrayView<const GO> basalFacesIDAV = Teuchos::arrayView(basalFacesID, NumBasalFaces);
Teuchos::ArrayView<const GO> topFacesIDAV = Teuchos::arrayView(topFacesID, NumBasalFaces);
Teuchos::ArrayView<const GO> westFacesIDAV = Teuchos::arrayView(westFacesID, NumWestFaces);
Teuchos::ArrayView<const GO> eastFacesIDAV = Teuchos::arrayView(eastFacesID, NumEastFaces);
Teuchos::ArrayView<const GO> southFacesIDAV = Teuchos::arrayView(southFacesID, NumSouthFaces);
Teuchos::ArrayView<const GO> northFacesIDAV = Teuchos::arrayView(northFacesID, NumNorthFaces);
//Distribute the elements according to the global element IDs
elem_mapT = Teuchos::rcp(new Tpetra_Map(NumEles, globalElesIDAV, 0, commT));
//Distribute the nodes according to the global node IDs
node_mapT = Teuchos::rcp(new Tpetra_Map(NumNodes, globalNodesIDAV, 0, commT));
//Distribute the elements according to the basal face IDs
basal_face_mapT = Teuchos::rcp(new Tpetra_Map(NumBasalFaces, basalFacesIDAV, 0, commT));
//Distribute the elements according to the top face IDs
top_face_mapT = Teuchos::rcp(new Tpetra_Map(NumBasalFaces, topFacesIDAV, 0, commT));
//Distribute the elements according to the lateral face IDs
west_face_mapT = Teuchos::rcp(new Tpetra_Map(NumWestFaces, westFacesIDAV, 0, commT));
east_face_mapT = Teuchos::rcp(new Tpetra_Map(NumEastFaces, eastFacesIDAV, 0, commT));
south_face_mapT = Teuchos::rcp(new Tpetra_Map(NumSouthFaces, southFacesIDAV, 0, commT));
north_face_mapT = Teuchos::rcp(new Tpetra_Map(NumNorthFaces, northFacesIDAV, 0, commT));
params->validateParameters(*getValidDiscretizationParameters(),0);
std::string ebn="Element Block 0";
partVec[0] = & metaData->declare_part(ebn, stk::topology::ELEMENT_RANK );
ebNameToIndex[ebn] = 0;
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*partVec[0]);
#endif
std::vector<std::string> nsNames;
std::string nsn="NodeSetDirichlet";
nsNames.push_back(nsn);
nsPartVec[nsn] = & metaData->declare_part(nsn, stk::topology::NODE_RANK );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*nsPartVec[nsn]);
#endif
std::vector<std::string> ssNames;
std::string ssnBasal="Basal";
std::string ssnTop="Top";
std::string ssnLateral="Lateral";
ssNames.push_back(ssnBasal);
ssNames.push_back(ssnTop);
ssNames.push_back(ssnLateral);
ssPartVec[ssnBasal] = & metaData->declare_part(ssnBasal, metaData->side_rank() );
ssPartVec[ssnTop] = & metaData->declare_part(ssnTop, metaData->side_rank() );
ssPartVec[ssnLateral] = & metaData->declare_part(ssnLateral, metaData->side_rank() );
#ifdef ALBANY_SEACAS
stk::io::put_io_part_attribute(*ssPartVec[ssnBasal]);
stk::io::put_io_part_attribute(*ssPartVec[ssnTop]);
stk::io::put_io_part_attribute(*ssPartVec[ssnLateral]);
#endif
stk::mesh::set_cell_topology<shards::Hexahedron<8> >(*partVec[0]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnBasal]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnTop]);
stk::mesh::set_cell_topology<shards::Quadrilateral<4> >(*ssPartVec[ssnLateral]);
numDim = 3;
int cub = params->get("Cubature Degree",3);
int worksetSizeMax = params->get("Workset Size",50);
int worksetSize = this->computeWorksetSize(worksetSizeMax, elem_mapT->getNodeNumElements());
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(),
ebNameToIndex, this->interleavedOrdering));
}
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();
}
}
#include <stk_mesh/fem/FEMHelpers.hpp>
#include <stk_mesh/fem/EntityRanks.hpp>
#include "Albany_Utils.hpp"
enum { field_data_chunk_size = 1001 };
Albany::FromCubitSTKMeshStruct::FromCubitSTKMeshStruct(
const Teuchos::RCP<CUTR::CubitMeshMover>& meshMover,
const Teuchos::RCP<Teuchos::ParameterList>& params,
const unsigned int neq_,
const Teuchos::RCP<Albany::StateInfoStruct>& sis,
) :
periodic(params->get("Periodic BC", false))
{
params->validateParameters(*getValidDiscretizationParameters(),0);
neq=neq_;
// Get singleton to STK info as loaded by Cubit MeshMover
STKMeshData* stkMeshData = STKMeshData::instance();
metaData = stkMeshData->get_meta_data();
coordinates_field = stkMeshData->get_coords_field();
solution_field = & metaData->declare_field< VectorFieldType >( "solution" );
residual_field = & metaData->declare_field< VectorFieldType >( "residual" );
stk::mesh::put_field( *solution_field , metaData->node_rank() , metaData->universal_part(), neq );
stk::mesh::put_field( *residual_field , metaData->node_rank() , metaData->universal_part() , neq );
// Construct nsPartVec from similar stkMeshData struct
std::map<int, stk::mesh::Part*> nsList= stkMeshData->get_nodeset_list();