Teuchos::RCP<PeridigmNS::NeighborhoodData> PeridigmNS::Block::createNeighborhoodDataFromGlobalNeighborhoodData(Teuchos::RCP<const Epetra_BlockMap> globalOverlapScalarPointMap,
Teuchos::RCP<const PeridigmNS::NeighborhoodData> globalNeighborhoodData)
{
int numOwnedPoints = ownedScalarPointMap->NumMyElements();
int* ownedPointGlobalIDs = ownedScalarPointMap->MyGlobalElements();
vector<int> ownedIDs(numOwnedPoints);
vector<int> neighborhoodList;
vector<int> neighborhoodPtr(numOwnedPoints);
int* const globalNeighborhoodList = globalNeighborhoodData->NeighborhoodList();
int* const globalNeighborhoodPtr = globalNeighborhoodData->NeighborhoodPtr();
// Create the neighborhoodList and neighborhoodPtr for this block.
// All the IDs in the neighborhoodList and neighborhoodPtr are local IDs into
// the block-specific overlap map.
for(int i=0 ; i<numOwnedPoints ; ++i){
neighborhoodPtr[i] = (int)(neighborhoodList.size());
int globalID = ownedPointGlobalIDs[i];
ownedIDs[i] = overlapScalarPointMap->LID(globalID);
int globalNeighborhoodListIndex = globalNeighborhoodPtr[globalOverlapScalarPointMap->LID(globalID)];
int numNeighbors = globalNeighborhoodList[globalNeighborhoodListIndex++];
neighborhoodList.push_back(numNeighbors);
for(int j=0 ; j<numNeighbors ; ++j){
int globalNeighborID = globalOverlapScalarPointMap->GID(globalNeighborhoodList[globalNeighborhoodListIndex++]);
neighborhoodList.push_back( overlapScalarPointMap->LID(globalNeighborID) );
}
}
// create the NeighborhoodData for this block
Teuchos::RCP<PeridigmNS::NeighborhoodData> blockNeighborhoodData = Teuchos::rcp(new PeridigmNS::NeighborhoodData);
blockNeighborhoodData->SetNumOwned(ownedIDs.size());
if(ownedIDs.size() > 0){
memcpy(blockNeighborhoodData->OwnedIDs(),
&ownedIDs.at(0),
ownedIDs.size()*sizeof(int));
}
if(neighborhoodPtr.size() > 0){
memcpy(blockNeighborhoodData->NeighborhoodPtr(),
&neighborhoodPtr.at(0),
neighborhoodPtr.size()*sizeof(int));
}
blockNeighborhoodData->SetNeighborhoodListSize(neighborhoodList.size());
if(neighborhoodList.size() > 0){
memcpy(blockNeighborhoodData->NeighborhoodList(),
&neighborhoodList.at(0),
neighborhoodList.size()*sizeof(int));
}
return blockNeighborhoodData;
}
// =============================================================================
Teuchos::RCP<Epetra_Vector>
VIO::EpetraMesh::Reader::
extractStateData_ ( const vtkSmartPointer<vtkDataSet> & vtkData,
const Teuchos::RCP<const Epetra_Comm> & comm
) const
{
vtkIdType numArrays = vtkData->GetPointData()->GetNumberOfArrays();
TEUCHOS_ASSERT_EQUALITY ( numArrays, 1 );
const vtkSmartPointer<vtkDataArray> & array =
vtkData->GetPointData()->GetArray(0);
vtkIdType numComponents = array->GetNumberOfComponents();
TEUCHOS_ASSERT_EQUALITY ( numComponents, 2 ); // for *complex* values
// this is the total number of grid points
vtkIdType numPoints = array->GetNumberOfTuples();
// Create maps.
// TODO They are created at another spot already. Avoid the work.
Teuchos::RCP<Epetra_Map> nodesMap = Teuchos::rcp( new Epetra_Map( numPoints, 0, *comm ) );
Teuchos::RCP<Epetra_Map> complexValuesMap = createComplexValuesMap_ ( *nodesMap );
Teuchos::RCP<Epetra_Vector> z =
Teuchos::rcp ( new Epetra_Vector ( *complexValuesMap ) );
// fill z
double val[2];
for ( int k = 0; k < nodesMap->NumMyElements(); k++ )
{
array->GetTuple( nodesMap->GID(k), val );
z->ReplaceMyValue( 2*k , 0, val[0] );
z->ReplaceMyValue( 2*k+1, 0, val[1] );
}
return z;
}
void
PeridigmNS::ElasticPlasticMaterial::computeAutomaticDifferentiationJacobian(const double dt,
const int numOwnedPoints,
const int* ownedIDs,
const int* neighborhoodList,
PeridigmNS::DataManager& dataManager,
PeridigmNS::SerialMatrix& jacobian,
PeridigmNS::Material::JacobianType jacobianType) const
{
// Compute contributions to the tangent matrix on an element-by-element basis
// To reduce memory re-allocation, use static variable to store Fad types for
// current coordinates (independent variables).
static vector<Sacado::Fad::DFad<double> > y_AD;
// Loop over all points.
int neighborhoodListIndex = 0;
for(int iID=0 ; iID<numOwnedPoints ; ++iID){
// Create a temporary neighborhood consisting of a single point and its neighbors.
int numNeighbors = neighborhoodList[neighborhoodListIndex++];
int numEntries = numNeighbors+1;
int numDof = 3*numEntries;
vector<int> tempMyGlobalIDs(numEntries);
// Put the node at the center of the neighborhood at the beginning of the list.
tempMyGlobalIDs[0] = dataManager.getOwnedScalarPointMap()->GID(iID);
vector<int> tempNeighborhoodList(numEntries);
tempNeighborhoodList[0] = numNeighbors;
for(int iNID=0 ; iNID<numNeighbors ; ++iNID){
int neighborID = neighborhoodList[neighborhoodListIndex++];
tempMyGlobalIDs[iNID+1] = dataManager.getOverlapScalarPointMap()->GID(neighborID);
tempNeighborhoodList[iNID+1] = iNID+1;
}
Epetra_SerialComm serialComm;
Teuchos::RCP<Epetra_BlockMap> tempOneDimensionalMap = Teuchos::rcp(new Epetra_BlockMap(numEntries, numEntries, &tempMyGlobalIDs[0], 1, 0, serialComm));
Teuchos::RCP<Epetra_BlockMap> tempThreeDimensionalMap = Teuchos::rcp(new Epetra_BlockMap(numEntries, numEntries, &tempMyGlobalIDs[0], 3, 0, serialComm));
Teuchos::RCP<Epetra_BlockMap> tempBondMap = Teuchos::rcp(new Epetra_BlockMap(1, 1, &tempMyGlobalIDs[0], numNeighbors, 0, serialComm));
// Create a temporary DataManager containing data for this point and its neighborhood.
PeridigmNS::DataManager tempDataManager;
tempDataManager.setMaps(Teuchos::RCP<const Epetra_BlockMap>(),
tempOneDimensionalMap,
Teuchos::RCP<const Epetra_BlockMap>(),
tempThreeDimensionalMap,
tempBondMap);
// The temporary data manager will have the same fields and data as the real data manager.
vector<int> fieldIds = dataManager.getFieldIds();
tempDataManager.allocateData(fieldIds);
tempDataManager.copyLocallyOwnedDataFromDataManager(dataManager);
// Set up numOwnedPoints and ownedIDs.
// There is only one owned ID, and it has local ID zero in the tempDataManager.
int tempNumOwnedPoints = 1;
vector<int> tempOwnedIDs(tempNumOwnedPoints);
tempOwnedIDs[0] = 0;
// Use the scratchMatrix as sub-matrix for storing tangent values prior to loading them into the global tangent matrix.
// Resize scratchMatrix if necessary
if(scratchMatrix.Dimension() < numDof)
scratchMatrix.Resize(numDof);
// Create a list of global indices for the rows/columns in the scratch matrix.
vector<int> globalIndices(numDof);
for(int i=0 ; i<numEntries ; ++i){
int globalID = tempOneDimensionalMap->GID(i);
for(int j=0 ; j<3 ; ++j)
globalIndices[3*i+j] = 3*globalID+j;
}
// Extract pointers to the underlying data in the constitutiveData array.
double *x, *y, *cellVolume, *weightedVolume, *damage, *bondDamage, *edpN, *lambdaN;
tempDataManager.getData(m_modelCoordinatesFieldId, PeridigmField::STEP_NONE)->ExtractView(&x);
tempDataManager.getData(m_coordinatesFieldId, PeridigmField::STEP_NP1)->ExtractView(&y);
tempDataManager.getData(m_volumeFieldId, PeridigmField::STEP_NONE)->ExtractView(&cellVolume);
tempDataManager.getData(m_weightedVolumeFieldId, PeridigmField::STEP_NONE)->ExtractView(&weightedVolume);
tempDataManager.getData(m_damageFieldId, PeridigmField::STEP_NP1)->ExtractView(&damage);
tempDataManager.getData(m_bondDamageFieldId, PeridigmField::STEP_NP1)->ExtractView(&bondDamage);
tempDataManager.getData(m_deviatoricPlasticExtensionFieldId, PeridigmField::STEP_N)->ExtractView(&edpN);
tempDataManager.getData(m_lambdaFieldId, PeridigmField::STEP_N)->ExtractView(&lambdaN);
// Create arrays of Fad objects for the current coordinates, dilatation, and force density
// Modify the existing vector of Fad objects for the current coordinates
if((int)y_AD.size() < numDof)
y_AD.resize(numDof);
for(int i=0 ; i<numDof ; ++i){
y_AD[i].diff(i, numDof);
y_AD[i].val() = y[i];
}
// Create vectors of empty AD types for the dependent variables
vector<Sacado::Fad::DFad<double> > dilatation_AD(numEntries);
vector<Sacado::Fad::DFad<double> > lambdaNP1_AD(numEntries);
int numBonds = tempDataManager.getData(m_deviatoricPlasticExtensionFieldId, PeridigmField::STEP_N)->MyLength();
vector<Sacado::Fad::DFad<double> > edpNP1(numBonds);
vector<Sacado::Fad::DFad<double> > force_AD(numDof);
// Evaluate the constitutive model using the AD types
MATERIAL_EVALUATION::computeDilatation(x,&y_AD[0],weightedVolume,cellVolume,bondDamage,&dilatation_AD[0],&tempNeighborhoodList[0],tempNumOwnedPoints,m_horizon);
MATERIAL_EVALUATION::computeInternalForceIsotropicElasticPlastic
(
x,
&y_AD[0],
weightedVolume,
cellVolume,
&dilatation_AD[0],
bondDamage,
edpN,
&edpNP1[0],
lambdaN,
&lambdaNP1_AD[0],
&force_AD[0],
&tempNeighborhoodList[0],
tempNumOwnedPoints,
m_bulkModulus,
m_shearModulus,
m_horizon,
m_yieldStress,
m_isPlanarProblem,
m_thickness);
// Load derivative values into scratch matrix
// Multiply by volume along the way to convert force density to force
for(int row=0 ; row<numDof ; ++row){
for(int col=0 ; col<numDof ; ++col){
scratchMatrix(row, col) = force_AD[row].dx(col) * cellVolume[row/3];
}
}
// Sum the values into the global tangent matrix (this is expensive).
jacobian.addValues((int)globalIndices.size(), &globalIndices[0], scratchMatrix.Data());
}
}
// The solve is done in the felix_driver_run function, and the solution is passed back to Glimmer-CISM
// IK, 12/3/13: time_inc_yr and cur_time_yr are not used here...
void felix_driver_run(FelixToGlimmer * ftg_ptr, double& cur_time_yr, double time_inc_yr)
{
//IK, 12/9/13: how come FancyOStream prints an all processors??
Teuchos::RCP<Teuchos::FancyOStream> out(Teuchos::VerboseObjectBase::getDefaultOStream());
if (debug_output_verbosity != 0 & mpiCommT->getRank() == 0) {
std::cout << "In felix_driver_run, cur_time, time_inc = " << cur_time_yr
<< " " << time_inc_yr << std::endl;
}
// ---------------------------------------------
// get u and v velocity solution from Glimmer-CISM
// IK, 11/26/13: need to concatenate these into a single solve for initial condition for Albany/FELIX solve
// IK, 3/14/14: moved this step to felix_driver_run from felix_driver init, since we still want to grab and u and v velocities for CISM if the mesh hasn't changed,
// in which case only felix_driver_run will be called, not felix_driver_init.
// ---------------------------------------------
if (debug_output_verbosity != 0 & mpiCommT->getRank() == 0)
std::cout << "In felix_driver_run: grabbing pointers to u and v velocities in CISM..." << std::endl;
uVel_ptr = ftg_ptr ->getDoubleVar("uvel", "velocity");
vVel_ptr = ftg_ptr ->getDoubleVar("vvel", "velocity");
// ---------------------------------------------
// Set restart solution to the one passed from CISM
// IK, 3/14/14: moved this from felix_driver_init to felix_driver_run.
// ---------------------------------------------
if (debug_output_verbosity != 0 & mpiCommT->getRank() == 0)
std::cout << "In felix_driver_run: setting initial condition from CISM..." << std::endl;
//Check what kind of ordering you have in the solution & create solutionField object.
interleavedOrdering = meshStruct->getInterleavedOrdering();
Albany::AbstractSTKFieldContainer::VectorFieldType* solutionField;
if(interleavedOrdering)
solutionField = Teuchos::rcp_dynamic_cast<Albany::OrdinarySTKFieldContainer<true> >(meshStruct->getFieldContainer())->getSolutionField();
else
solutionField = Teuchos::rcp_dynamic_cast<Albany::OrdinarySTKFieldContainer<false> >(meshStruct->getFieldContainer())->getSolutionField();
//Create vector used to renumber nodes on each processor from the Albany convention (horizontal levels first) to the CISM convention (vertical layers first)
nNodes2D = (global_ewn + 1)*(global_nsn+1); //number global nodes in the domain in 2D
nNodesProc2D = (nsn-2*nhalo+1)*(ewn-2*nhalo+1); //number of nodes on each processor in 2D
cismToAlbanyNodeNumberMap.resize(upn*nNodesProc2D);
for (int j=0; j<nsn-2*nhalo+1;j++) {
for (int i=0; i<ewn-2*nhalo+1; i++) {
for (int k=0; k<upn; k++) {
int index = k+upn*i + j*(ewn-2*nhalo+1)*upn;
cismToAlbanyNodeNumberMap[index] = k*nNodes2D + global_node_id_owned_map_Ptr[i+j*(ewn-2*nhalo+1)];
//if (mpiComm->MyPID() == 0)
// std::cout << "index: " << index << ", cismToAlbanyNodeNumberMap: " << cismToAlbanyNodeNumberMap[index] << std::endl;
}
}
}
//The way it worked out, uVel_ptr and vVel_ptr have more nodes than the nodes in the mesh passed to Albany/CISM for the solve. In particular,
//there is 1 row of halo elements in uVel_ptr and vVel_ptr. To account for this, we copy uVel_ptr and vVel_ptr into std::vectors, which do not have the halo elements.
std::vector<double> uvel_vec(upn*nNodesProc2D);
std::vector<double> vvel_vec(upn*nNodesProc2D);
int counter1 = 0;
int counter2 = 0;
int local_nodeID;
for (int j=0; j<nsn-1; j++) {
for (int i=0; i<ewn-1; i++) {
for (int k=0; k<upn; k++) {
if (j >= nhalo-1 & j < nsn-nhalo) {
if (i >= nhalo-1 & i < ewn-nhalo) {
#ifdef CISM_USE_EPETRA
local_nodeID = node_map->LID(cismToAlbanyNodeNumberMap[counter1]);
#else
local_nodeID = node_map->getLocalElement(cismToAlbanyNodeNumberMap[counter1]);
#endif
uvel_vec[counter1] = uVel_ptr[counter2];
vvel_vec[counter1] = vVel_ptr[counter2];
counter1++;
}
}
counter2++;
}
}
}
//Loop over all the elements to find which nodes are active. For the active nodes, copy uvel and vvel from CISM into Albany solution array to
//use as initial condition.
//NOTE: there is some inefficiency here by looping over all the elements. TO DO? pass only active nodes from Albany-CISM to improve this?
double velScale = seconds_per_year*vel_scaling_param;
for (int i=0; i<nElementsActive; i++) {
for (int j=0; j<8; j++) {
int node_GID = global_element_conn_active_Ptr[i + nElementsActive*j]; //node_GID is 1-based
#ifdef CISM_USE_EPETRA
int node_LID = node_map->LID(node_GID); //node_LID is 0-based
#else
int node_LID = node_map->getLocalElement(node_GID); //node_LID is 0-based
#endif
stk::mesh::Entity node = meshStruct->bulkData->get_entity(stk::topology::NODE_RANK, node_GID);
double* sol = stk::mesh::field_data(*solutionField, node);
//IK, 3/18/14: added division by velScale to convert uvel and vvel from dimensionless to having units of m/year (the Albany units)
sol[0] = uvel_vec[node_LID]/velScale;
sol[1] = vvel_vec[node_LID]/velScale;
}
}
// ---------------------------------------------------------------------------------------------------
// Solve
// ---------------------------------------------------------------------------------------------------
if (debug_output_verbosity != 0 & mpiCommT->getRank() == 0)
std::cout << "In felix_driver_run: starting the solve... " << std::endl;
//Need to set HasRestart solution such that uvel_Ptr and vvel_Ptr (u and v from Glimmer/CISM) are always set as initial condition?
meshStruct->setHasRestartSolution(!first_time_step);
//Turn off homotopy if we're not in the first time-step.
//NOTE - IMPORTANT: Glen's Law Homotopy parameter should be set to 1.0 in the parameter list for this logic to work!!!
if (!first_time_step)
{
meshStruct->setRestartDataTime(parameterList->sublist("Problem").get("Homotopy Restart Step", 1.));
double homotopy = parameterList->sublist("Problem").sublist("FELIX Viscosity").get("Glen's Law Homotopy Parameter", 1.0);
if(meshStruct->restartDataTime()== homotopy) {
parameterList->sublist("Problem").set("Solution Method", "Steady");
parameterList->sublist("Piro").set("Solver Type", "NOX");
}
}
albanyApp->createDiscretization();
//IK, 10/30/14: Check that # of elements from previous time step hasn't changed.
//If it has not, use previous solution as initial guess for current time step.
//Otherwise do not set initial solution. It's possible this can be improved so some part of the previous solution is used
//defined on the current mesh (if it receded, which likely it will in dynamic ice sheet simulations...).
if (nElementsActivePrevious != nElementsActive) previousSolution = Teuchos::null;
albanyApp->finalSetUp(parameterList, previousSolution);
//if (!first_time_step)
// std::cout << "previousSolution: " << *previousSolution << std::endl;
#ifdef CISM_USE_EPETRA
solver = slvrfctry->createThyraSolverAndGetAlbanyApp(albanyApp, mpiComm, mpiComm, Teuchos::null, false);
#else
solver = slvrfctry->createAndGetAlbanyAppT(albanyApp, mpiCommT, mpiCommT, Teuchos::null, false);
#endif
Teuchos::ParameterList solveParams;
solveParams.set("Compute Sensitivities", true);
Teuchos::Array<Teuchos::RCP<const Thyra::VectorBase<double> > > thyraResponses;
Teuchos::Array<Teuchos::Array<Teuchos::RCP<const Thyra::MultiVectorBase<double> > > > thyraSensitivities;
Piro::PerformSolveBase(*solver, solveParams, thyraResponses, thyraSensitivities);
#ifdef CISM_USE_EPETRA
const Epetra_Map& ownedMap(*albanyApp->getDiscretization()->getMap()); //owned map
const Epetra_Map& overlapMap(*albanyApp->getDiscretization()->getOverlapMap()); //overlap map
Epetra_Import import(overlapMap, ownedMap); //importer from ownedMap to overlapMap
Epetra_Vector solutionOverlap(overlapMap); //overlapped solution
solutionOverlap.Import(*albanyApp->getDiscretization()->getSolutionField(), import, Insert);
#else
Teuchos::RCP<const Tpetra_Map> ownedMap = albanyApp->getDiscretization()->getMapT(); //owned map
Teuchos::RCP<const Tpetra_Map> overlapMap = albanyApp->getDiscretization()->getOverlapMapT(); //overlap map
Teuchos::RCP<Tpetra_Import> import = Teuchos::rcp(new Tpetra_Import(ownedMap, overlapMap));
Teuchos::RCP<Tpetra_Vector> solutionOverlap = Teuchos::rcp(new Tpetra_Vector(overlapMap));
solutionOverlap->doImport(*albanyApp->getDiscretization()->getSolutionFieldT(), *import, Tpetra::INSERT);
Teuchos::ArrayRCP<const ST> solutionOverlap_constView = solutionOverlap->get1dView();
#endif
#ifdef WRITE_TO_MATRIX_MARKET
#ifdef CISM_USE_EPETRA
//For debug: write solution and maps to matrix market file
EpetraExt::BlockMapToMatrixMarketFile("node_map.mm", *node_map);
EpetraExt::BlockMapToMatrixMarketFile("map.mm", ownedMap);
EpetraExt::BlockMapToMatrixMarketFile("overlap_map.mm", overlapMap);
EpetraExt::MultiVectorToMatrixMarketFile("solution.mm", *albanyApp->getDiscretization()->getSolutionField());
#else
Tpetra_MatrixMarket_Writer::writeMapFile("node_map.mm", *node_map);
Tpetra_MatrixMarket_Writer::writeMapFile("map.mm", *ownedMap);
Tpetra_MatrixMarket_Writer::writeMapFile("overlap_map.mm", *overlapMap);
Tpetra_MatrixMarket_Writer::writeDenseFile("solution.mm", app->getDiscretization()->getSolutionFieldT());
#endif
#endif
//set previousSolution (used as initial guess for next time step) to final Albany solution.
previousSolution = Teuchos::rcp(new Tpetra_Vector(*albanyApp->getDiscretization()->getSolutionFieldT()));
nElementsActivePrevious = nElementsActive;
//std::cout << "Final solution: " << *albanyApp->getDiscretization()->getSolutionField() << std::endl;
// ---------------------------------------------------------------------------------------------------
// Compute sensitivies / responses and perform regression tests
// IK, 12/9/13: how come this is turned off in mpas branch?
// ---------------------------------------------------------------------------------------------------
if (debug_output_verbosity != 0 & mpiCommT->getRank() == 0)
std::cout << "Computing responses and sensitivities..." << std::endl;
int status=0; // 0 = pass, failures are incremented
#ifdef CISM_USE_EPETRA
Teuchos::Array<Teuchos::RCP<const Epetra_Vector> > responses;
Teuchos::Array<Teuchos::Array<Teuchos::RCP<const Epetra_MultiVector> > > sensitivities;
epetraFromThyra(mpiComm, thyraResponses, thyraSensitivities, responses, sensitivities);
#else
Teuchos::Array<Teuchos::RCP<const Tpetra_Vector> > responses;
Teuchos::Array<Teuchos::Array<Teuchos::RCP<const Tpetra_MultiVector> > > sensitivities;
tpetraFromThyra(thyraResponses, thyraSensitivities, responses, sensitivities);
#endif
const int num_p = solver->Np(); // Number of *vectors* of parameters
const int num_g = solver->Ng(); // Number of *vectors* of responses
if (debug_output_verbosity != 0) {
*out << "Finished eval of first model: Params, Responses "
<< std::setprecision(12) << std::endl;
}
const Thyra::ModelEvaluatorBase::InArgs<double> nominal = solver->getNominalValues();
if (debug_output_verbosity != 0) {
for (int i=0; i<num_p; i++) {
#ifdef CISM_USE_EPETRA
const Teuchos::RCP<const Epetra_Vector> p_init = epetraVectorFromThyra(mpiComm, nominal.get_p(i));
p_init->Print(*out << "\nParameter vector " << i << ":\n");
#else
Albany::printTpetraVector(*out << "\nParameter vector " << i << ":\n",
ConverterT::getConstTpetraVector(nominal.get_p(i)));
#endif
}
}
for (int i=0; i<num_g-1; i++) {
#ifdef CISM_USE_EPETRA
const Teuchos::RCP<const Epetra_Vector> g = responses[i];
#else
const Teuchos::RCP<const Tpetra_Vector> g = responses[i];
#endif
bool is_scalar = true;
if (albanyApp != Teuchos::null)
is_scalar = albanyApp->getResponse(i)->isScalarResponse();
if (is_scalar) {
if (debug_output_verbosity != 0) {
#ifdef CISM_USE_EPETRA
g->Print(*out << "\nResponse vector " << i << ":\n");
#else
Albany::printTpetraVector(*out << "\nResponse vector " << i << ":\n", g);
#endif
}
if (num_p == 0 && cur_time_yr == final_time) {
// Just calculate regression data -- only if in final time step
#ifdef CISM_USE_EPETRA
status += slvrfctry->checkSolveTestResults(i, 0, g.get(), NULL);
#else
status += slvrfctry->checkSolveTestResultsT(i, 0, g.get(), NULL);
#endif
} else {
for (int j=0; j<num_p; j++) {
#ifdef CISM_USE_EPETRA
const Teuchos::RCP<const Epetra_MultiVector> dgdp = sensitivities[i][j];
#else
const Teuchos::RCP<const Tpetra_MultiVector> dgdp = sensitivities[i][j];
#endif
if (debug_output_verbosity != 0) {
if (Teuchos::nonnull(dgdp)) {
#ifdef CISM_USE_EPETRA
dgdp->Print(*out << "\nSensitivities (" << i << "," << j << "):!\n");
#else
Albany::printTpetraVector(*out << "\nSensitivities (" << i << "," << j << "):!\n", dgdp);
#endif
}
}
if (cur_time_yr == final_time) {
#ifdef CISM_USE_EPETRA
status += slvrfctry->checkSolveTestResults(i, j, g.get(), dgdp.get());
#else
status += slvrfctry->checkSolveTestResultsT(i, j, g.get(), dgdp.get());
#endif
}
}
}
}
}
if (debug_output_verbosity != 0 && cur_time_yr == final_time) //only print regression test result if you're in the final time step
*out << "\nNumber of Failed Comparisons: " << status << std::endl;
//IK, 10/30/14: added the following line so that when you run ctest from CISM the test fails if there are some failed comparisons.
if (status > 0)
TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error, "All regression comparisons did not pass!" << std::endl);
// ---------------------------------------------------------------------------------------------------
// Copy solution back to glimmer uvel and vvel arrays to be passed back
// ---------------------------------------------------------------------------------------------------
//std::cout << "overlapMap # global elements: " << overlapMap.NumGlobalElements() << std::endl;
//std::cout << "overlapMap # my elements: " << overlapMap.NumMyElements() << std::endl;
//std::cout << "overlapMap: " << overlapMap << std::endl;
//std::cout << "map # global elements: " << ownedMap.NumGlobalElements() << std::endl;
//std::cout << "map # my elements: " << ownedMap.NumMyElements() << std::endl;
//std::cout << "node_map # global elements: " << node_map->NumGlobalElements() << std::endl;
//std::cout << "node_map # my elements: " << node_map->NumMyElements() << std::endl;
//std::cout << "node_map: " << *node_map << std::endl;
if (debug_output_verbosity != 0 & mpiCommT->getRank() == 0)
std::cout << "In felix_driver_run: copying Albany solution to uvel and vvel to send back to CISM... " << std::endl;
#ifdef CISM_USE_EPETRA
//Epetra_Vectors to hold uvel and vvel to be passed to Glimmer/CISM
Epetra_Vector uvel(*node_map, true);
Epetra_Vector vvel(*node_map, true);
#else
//Tpetra_Vectors to hold uvel and vvel to be passed to Glimmer/CISM
Teuchos::RCP<Tpetra_Vector> uvel = Teuchos::rcp(new Tpetra_Vector(node_map, true));
Teuchos::RCP<Tpetra_Vector> vvel = Teuchos::rcp(new Tpetra_Vector(node_map, true));
#endif
#ifdef CISM_USE_EPETRA
if (interleavedOrdering == true) {
for (int i=0; i<overlapMap.NumMyElements(); i++) {
int global_dof = overlapMap.GID(i);
double sol_value = solutionOverlap[i];
int modulo = (global_dof % 2); //check if dof is for u or for v
int vel_global_dof, vel_local_dof;
if (modulo == 0) { //u dof
vel_global_dof = global_dof/2+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->LID(vel_global_dof); //look up local id corresponding to global id in node_map
//std::cout << "uvel: global_dof = " << global_dof << ", uvel_global_dof = " << vel_global_dof << ", uvel_local_dof = " << vel_local_dof << std::endl;
uvel.ReplaceMyValues(1, &sol_value, &vel_local_dof);
}
else { // v dof
vel_global_dof = (global_dof-1)/2+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->LID(vel_global_dof); //look up local id corresponding to global id in node_map
vvel.ReplaceMyValues(1, &sol_value, & vel_local_dof);
}
}
}
else { //note: the case with non-interleaved ordering has not been tested...
int numDofs = overlapMap.NumGlobalElements();
for (int i=0; i<overlapMap.NumMyElements(); i++) {
int global_dof = overlapMap.GID(i);
double sol_value = solutionOverlap[i];
int vel_global_dof, vel_local_dof;
if (global_dof < numDofs/2) { //u dof
vel_global_dof = global_dof+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->LID(vel_global_dof); //look up local id corresponding to global id in node_map
uvel.ReplaceMyValues(1, &sol_value, &vel_local_dof);
}
else { //v dofs
vel_global_dof = global_dof-numDofs/2+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->LID(vel_global_dof); //look up local id corresponding to global id in node_map
vvel.ReplaceMyValues(1, &sol_value, & vel_local_dof);
}
}
}
#else
if (interleavedOrdering == true) {
for (int i=0; i<overlapMap->getNodeNumElements(); i++) {
int global_dof = overlapMap->getGlobalElement(i);
double sol_value = solutionOverlap_constView[i];
int modulo = (global_dof % 2); //check if dof is for u or for v
int vel_global_dof, vel_local_dof;
if (modulo == 0) { //u dof
vel_global_dof = global_dof/2+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->getLocalElement(vel_global_dof); //look up local id corresponding to global id in node_map
//std::cout << "uvel: global_dof = " << global_dof << ", uvel_global_dof = " << vel_global_dof << ", uvel_local_dof = " << vel_local_dof << std::endl;
uvel->replaceLocalValue(vel_local_dof, sol_value);
}
else { // v dof
vel_global_dof = (global_dof-1)/2+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->getLocalElement(vel_global_dof); //look up local id corresponding to global id in node_map
vvel->replaceLocalValue(vel_local_dof, sol_value);
}
}
}
else { //note: the case with non-interleaved ordering has not been tested...
int numDofs = overlapMap->getGlobalNumElements();
for (int i=0; i<overlapMap->getNodeNumElements(); i++) {
int global_dof = overlapMap->getGlobalElement(i);
double sol_value = solutionOverlap_constView[i];
int vel_global_dof, vel_local_dof;
if (global_dof < numDofs/2) { //u dof
vel_global_dof = global_dof+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->getLocalElement(vel_global_dof); //look up local id corresponding to global id in node_map
uvel->replaceLocalValue(vel_local_dof, sol_value);
}
else { //v dofs
vel_global_dof = global_dof-numDofs/2+1; //add 1 because node_map is 1-based
vel_local_dof = node_map->getLocalElement(vel_global_dof); //look up local id corresponding to global id in node_map
vvel->replaceLocalValue(vel_local_dof, sol_value);
}
}
}
#endif
#ifdef WRITE_TO_MATRIX_MARKET
//For debug: write solution to matrix market file
#ifdef CISM_USE_EPETRA
EpetraExt::MultiVectorToMatrixMarketFile("uvel.mm", uvel);
EpetraExt::MultiVectorToMatrixMarketFile("vvel.mm", vvel);
#else
Tpetra_MatrixMarket_Writer::writeDenseFile("uvel.mm", uvel);
Tpetra_MatrixMarket_Writer::writeDenseFile("vvel.mm", vvel);
#endif
#endif
//Copy uvel and vvel into uVel_ptr and vVel_ptr respectively (the arrays passed back to CISM) according to the numbering consistent w/ CISM.
counter1 = 0;
counter2 = 0;
#ifdef CISM_USE_EPETRA
#else
Teuchos::ArrayRCP<const ST> uvel_constView = uvel->get1dView();
Teuchos::ArrayRCP<const ST> vvel_constView = vvel->get1dView();
#endif
local_nodeID = 0;
for (int j=0; j<nsn-1; j++) {
for (int i=0; i<ewn-1; i++) {
for (int k=0; k<upn; k++) {
if (j >= nhalo-1 & j < nsn-nhalo) {
if (i >= nhalo-1 & i < ewn-nhalo) {
#ifdef CISM_USE_EPETRA
local_nodeID = node_map->LID(cismToAlbanyNodeNumberMap[counter1]);
//if (mpiComm->MyPID() == 0)
//std::cout << "counter1:" << counter1 << ", cismToAlbanyNodeNumberMap[counter1]: " << cismToAlbanyNodeNumberMap[counter1] << ", local_nodeID: "
//<< local_nodeID << ", uvel: " << uvel[local_nodeID] << std::endl; //uvel[local_nodeID] << std::endl;
uVel_ptr[counter2] = uvel[local_nodeID];
vVel_ptr[counter2] = vvel[local_nodeID];
#else
local_nodeID = node_map->getLocalElement(cismToAlbanyNodeNumberMap[counter1]);
uVel_ptr[counter2] = uvel_constView[local_nodeID];
vVel_ptr[counter2] = vvel_constView[local_nodeID];
#endif
counter1++;
}
}
else {
uVel_ptr[counter2] = 0.0;
vVel_ptr[counter2] = 0.0;
}
counter2++;
}
}
}
first_time_step = false;
}
TEUCHOS_UNIT_TEST(interlaced_op, test)
{
#ifdef HAVE_MPI
Teuchos::RCP<const Epetra_Comm> comm = Teuchos::rcp(new Epetra_MpiComm(MPI_COMM_WORLD));
#else
Teuchos::RCP<const Epetra_Comm> comm = Teuchos::rcp(new Epetra_SerialComm);
#endif
//int rank = comm->MyPID();
int numProc = comm->NumProc();
int num_KL = 1;
int porder = 5;
bool full_expansion = false;
Teuchos::RCP<const Stokhos::CompletePolynomialBasis<int,double> > basis = buildBasis(num_KL,porder);
Teuchos::RCP<Stokhos::Sparse3Tensor<int,double> > Cijk;
Teuchos::RCP<Stokhos::ParallelData> sg_parallel_data;
Teuchos::RCP<Stokhos::OrthogPolyExpansion<int,double> > expansion;
{
if(full_expansion)
Cijk = basis->computeTripleProductTensor();
else
Cijk = basis->computeLinearTripleProductTensor();
Teuchos::ParameterList parallelParams;
parallelParams.set("Number of Spatial Processors", numProc);
sg_parallel_data = Teuchos::rcp(new Stokhos::ParallelData(basis, Cijk, comm,
parallelParams));
expansion = Teuchos::rcp(new Stokhos::AlgebraicOrthogPolyExpansion<int,double>(basis,
Cijk));
}
Teuchos::RCP<const EpetraExt::MultiComm> sg_comm = sg_parallel_data->getMultiComm();
// determinstic PDE graph
Teuchos::RCP<Epetra_Map> determRowMap = Teuchos::rcp(new Epetra_Map(-1,10,0,*comm));
Teuchos::RCP<Epetra_CrsGraph> determGraph = Teuchos::rcp(new Epetra_CrsGraph(Copy,*determRowMap,1));
for(int row=0;row<determRowMap->NumMyElements();row++) {
int gid = determRowMap->GID(row);
determGraph->InsertGlobalIndices(gid,1,&gid);
}
for(int row=1;row<determRowMap->NumMyElements()-1;row++) {
int gid = determRowMap->GID(row);
int indices[2] = {gid-1,gid+1};
determGraph->InsertGlobalIndices(gid,2,indices);
}
determGraph->FillComplete();
Teuchos::RCP<Teuchos::ParameterList> params = Teuchos::rcp(new Teuchos::ParameterList);
params->set("Scale Operator by Inverse Basis Norms", false);
params->set("Include Mean", true);
params->set("Only Use Linear Terms", false);
Teuchos::RCP<Stokhos::EpetraSparse3Tensor> epetraCijk =
Teuchos::rcp(new Stokhos::EpetraSparse3Tensor(basis,Cijk,sg_comm));
Teuchos::RCP<Stokhos::EpetraOperatorOrthogPoly> W_sg_blocks =
Teuchos::rcp(new Stokhos::EpetraOperatorOrthogPoly(basis, epetraCijk->getStochasticRowMap(), determRowMap, determRowMap, sg_comm));
for(int i=0; i<W_sg_blocks->size(); i++) {
Teuchos::RCP<Epetra_CrsMatrix> crsMat = Teuchos::rcp(new Epetra_CrsMatrix(Copy,*determGraph));
crsMat->PutScalar(1.0 + i);
W_sg_blocks->setCoeffPtr(i,crsMat); // allocate a bunch of matrices
}
Teuchos::RCP<const Epetra_Map> sg_map =
Teuchos::rcp(EpetraExt::BlockUtility::GenerateBlockMap(
*determRowMap, *(epetraCijk->getStochasticRowMap()),
*(epetraCijk->getMultiComm())));
// build an interlaced operator (object under test) and a benchmark
// fully assembled operator
///////////////////////////////////////////////////////////////////////
Stokhos::InterlacedOperator op(sg_comm,basis,epetraCijk,determGraph,params);
op.PutScalar(0.0);
op.setupOperator(W_sg_blocks);
Stokhos::FullyAssembledOperator full_op(sg_comm,basis,epetraCijk,determGraph,sg_map,sg_map,params);
full_op.PutScalar(0.0);
full_op.setupOperator(W_sg_blocks);
// here we test interlaced operator against the fully assembled operator
///////////////////////////////////////////////////////////////////////
bool result = true;
for(int i=0;i<100;i++) {
// build vector for fully assembled operator (blockwise)
Teuchos::RCP<Stokhos::EpetraVectorOrthogPoly> x_vec_blocks =
Teuchos::rcp(new Stokhos::EpetraVectorOrthogPoly(basis,epetraCijk->getStochasticRowMap(),determRowMap,epetraCijk->getMultiComm()));
Teuchos::RCP<Stokhos::EpetraVectorOrthogPoly> f_vec_blocks =
Teuchos::rcp(new Stokhos::EpetraVectorOrthogPoly(basis,epetraCijk->getStochasticRowMap(),determRowMap,epetraCijk->getMultiComm()));
Teuchos::RCP<Epetra_Vector> x_vec_blocked = x_vec_blocks->getBlockVector();
Teuchos::RCP<Epetra_Vector> f_vec_blocked = f_vec_blocks->getBlockVector();
x_vec_blocked->Random(); // build an initial vector
f_vec_blocked->PutScalar(0.0);
// build interlaced vectors
Teuchos::RCP<Epetra_Vector> x_vec_inter = Teuchos::rcp(new Epetra_Vector(op.OperatorDomainMap()));
Teuchos::RCP<Epetra_Vector> f_vec_inter = Teuchos::rcp(new Epetra_Vector(op.OperatorRangeMap()));
Teuchos::RCP<Epetra_Vector> f_vec_blk_inter = Teuchos::rcp(new Epetra_Vector(op.OperatorRangeMap()));
Stokhos::SGModelEvaluator_Interlaced::copyToInterlacedVector(*x_vec_blocks,*x_vec_inter); // copy random x to
f_vec_inter->PutScalar(0.0);
full_op.Apply(*x_vec_blocked,*f_vec_blocked);
op.Apply(*x_vec_inter,*f_vec_inter);
// copy blocked action to interlaced for comparison
Stokhos::SGModelEvaluator_Interlaced::copyToInterlacedVector(*f_vec_blocks,*f_vec_blk_inter);
// compute norm
double error = 0.0;
double true_norm = 0.0;
f_vec_blk_inter->NormInf(&true_norm);
f_vec_blk_inter->Update(-1.0,*f_vec_inter,1.0);
f_vec_blk_inter->NormInf(&error);
out << "rel error = " << error/true_norm << " ( " << true_norm << " ), ";
result &= (error/true_norm < 1e-14);
}
out << std::endl;
TEST_ASSERT(result);
}
void PeridigmNS::Block::createMapsFromGlobalMaps(Teuchos::RCP<const Epetra_BlockMap> globalOwnedScalarPointMap,
Teuchos::RCP<const Epetra_BlockMap> globalOverlapScalarPointMap,
Teuchos::RCP<const Epetra_BlockMap> globalOwnedVectorPointMap,
Teuchos::RCP<const Epetra_BlockMap> globalOverlapVectorPointMap,
Teuchos::RCP<const Epetra_BlockMap> globalOwnedScalarBondMap,
Teuchos::RCP<const Epetra_Vector> globalBlockIds,
Teuchos::RCP<const PeridigmNS::NeighborhoodData> globalNeighborhoodData,
Teuchos::RCP<const PeridigmNS::NeighborhoodData> globalContactNeighborhoodData)
{
double* globalBlockIdsPtr;
globalBlockIds->ExtractView(&globalBlockIdsPtr);
// Create a list of all the on-processor elements that are part of this block
vector<int> IDs;
IDs.reserve(globalOverlapScalarPointMap->NumMyElements()); // upper bound
vector<int> bondIDs;
bondIDs.reserve(globalOverlapScalarPointMap->NumMyElements());
vector<int> bondElementSize;
bondElementSize.reserve(globalOwnedScalarPointMap->NumMyElements());
for(int iLID=0 ; iLID<globalOwnedScalarPointMap->NumMyElements() ; ++iLID){
if(globalBlockIdsPtr[iLID] == blockID) {
int globalID = globalOwnedScalarPointMap->GID(iLID);
IDs.push_back(globalID);
}
}
// Record the size of these elements in the bond map
// Note that if an element has no bonds, it has no entry in the bondMap
// So, the bond map and the scalar map can have a different number of entries (different local IDs)
for(int iLID=0 ; iLID<globalOwnedScalarBondMap->NumMyElements() ; ++iLID){
int globalID = globalOwnedScalarBondMap->GID(iLID);
int localID = globalOwnedScalarPointMap->LID(globalID);
if(globalBlockIdsPtr[localID] == blockID){
bondIDs.push_back(globalID);
bondElementSize.push_back(globalOwnedScalarBondMap->ElementSize(iLID));
}
}
// Create the owned scalar point map, the owned vector point map, and the owned scalar bond map
int numGlobalElements = -1;
int numMyElements = IDs.size();
int* myGlobalElements = 0;
if(numMyElements > 0)
myGlobalElements = &IDs.at(0);
int elementSize = 1;
int indexBase = 0;
ownedScalarPointMap =
Teuchos::rcp(new Epetra_BlockMap(numGlobalElements, numMyElements, myGlobalElements, elementSize, indexBase, globalOwnedScalarPointMap->Comm()));
elementSize = 3;
ownedVectorPointMap =
Teuchos::rcp(new Epetra_BlockMap(numGlobalElements, numMyElements, myGlobalElements, elementSize, indexBase, globalOwnedScalarPointMap->Comm()));
numMyElements = bondElementSize.size();
myGlobalElements = 0;
int* elementSizeList = 0;
if(numMyElements > 0){
myGlobalElements = &bondIDs.at(0);
elementSizeList = &bondElementSize.at(0);
}
ownedScalarBondMap =
Teuchos::rcp(new Epetra_BlockMap(numGlobalElements, numMyElements, myGlobalElements, elementSizeList, indexBase, globalOwnedScalarPointMap->Comm()));
// Create a list of nodes that need to be ghosted (both across material boundaries and across processor boundaries)
set<int> ghosts;
// Check the neighborhood list for things that need to be ghosted
int* const globalNeighborhoodList = globalNeighborhoodData->NeighborhoodList();
int globalNeighborhoodListIndex = 0;
for(int iLID=0 ; iLID<globalNeighborhoodData->NumOwnedPoints() ; ++iLID){
int numNeighbors = globalNeighborhoodList[globalNeighborhoodListIndex++];
if(globalBlockIdsPtr[iLID] == blockID) {
for(int i=0 ; i<numNeighbors ; ++i){
int neighborGlobalID = globalOverlapScalarPointMap->GID( globalNeighborhoodList[globalNeighborhoodListIndex + i] );
ghosts.insert(neighborGlobalID);
}
}
globalNeighborhoodListIndex += numNeighbors;
}
// Check the contact neighborhood list for things that need to be ghosted
if(!globalContactNeighborhoodData.is_null()){
int* const globalContactNeighborhoodList = globalContactNeighborhoodData->NeighborhoodList();
int globalContactNeighborhoodListIndex = 0;
for(int iLID=0 ; iLID<globalContactNeighborhoodData->NumOwnedPoints() ; ++iLID){
int numNeighbors = globalContactNeighborhoodList[globalContactNeighborhoodListIndex++];
if(globalBlockIdsPtr[iLID] == blockID) {
for(int i=0 ; i<numNeighbors ; ++i){
int neighborGlobalID = globalOverlapScalarPointMap->GID( globalContactNeighborhoodList[globalContactNeighborhoodListIndex + i] );
ghosts.insert(neighborGlobalID);
}
}
globalContactNeighborhoodListIndex += numNeighbors;
}
}
// Remove entries from ghosts that are already in IDs
for(unsigned int i=0 ; i<IDs.size() ; ++i)
ghosts.erase(IDs[i]);
// Copy IDs, this is the owned global ID list
vector<int> ownedIDs(IDs.begin(), IDs.end());
// Append ghosts to IDs
// This creates the overlap global ID list
for(set<int>::iterator it=ghosts.begin() ; it!=ghosts.end() ; ++it)
IDs.push_back(*it);
// Create the overlap scalar point map and the overlap vector point map
numMyElements = IDs.size();
myGlobalElements = 0;
if(numMyElements > 0)
myGlobalElements = &IDs.at(0);
elementSize = 1;
overlapScalarPointMap =
Teuchos::rcp(new Epetra_BlockMap(numGlobalElements, numMyElements, myGlobalElements, elementSize, indexBase, globalOwnedScalarPointMap->Comm()));
elementSize = 3;
overlapVectorPointMap =
Teuchos::rcp(new Epetra_BlockMap(numGlobalElements, numMyElements, myGlobalElements, elementSize, indexBase, globalOwnedScalarPointMap->Comm()));
// Invalidate the importers
oneDimensionalImporter = Teuchos::RCP<Epetra_Import>();
threeDimensionalImporter = Teuchos::RCP<Epetra_Import>();
}
// =============================================================================
Teuchos::RCP<VIO::EpetraMesh::Mesh>
VIO::EpetraMesh::Reader::
extractMeshData_( const vtkSmartPointer<vtkUnstructuredGrid> & vtkMesh,
const Teuchos::RCP<const Epetra_Comm> & comm
) const
{
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// create the maps based on the number of points
int numPoints = vtkMesh->GetNumberOfPoints();
Teuchos::RCP<Epetra_Map> nodesMap = Teuchos::rcp( new Epetra_Map( numPoints, 0, *comm ) );
Teuchos::RCP<Epetra_Map> complexValuesMap = createComplexValuesMap_ ( *nodesMap );
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Teuchos::RCP<Mesh> mesh = Teuchos::rcp( new Mesh( nodesMap,
complexValuesMap
)
);
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// get points
Teuchos::ArrayRCP<Point> points( numPoints );
for ( unsigned int k=0; k<numPoints; k++ )
vtkMesh->GetPoint( k, points[k].getRawPtr() );
mesh->setNodes( points );
// for ( int k=0; k<points.size(); k++ )
// std::cout << points[k] << std::endl;
// std::cout << "VVV" << std::endl;
// vtkMesh->Print( std::cout );
// determine the boundary points
// transform vtkMesh into vtkPolyData
vtkSmartPointer<vtkDataSetSurfaceFilter> surfaceFilter =
vtkSmartPointer<vtkDataSetSurfaceFilter>::New();
surfaceFilter->SetInput(vtkMesh);
surfaceFilter->Update();
// vtkPolyData* polydata = surfaceFilter->GetOutput();
// filter out the boundary edges
vtkFeatureEdges * pEdges = vtkFeatureEdges::New();
pEdges->SetInput( surfaceFilter->GetOutput() );
pEdges->BoundaryEdgesOn();
pEdges->FeatureEdgesOff();
pEdges->NonManifoldEdgesOff();
pEdges->ManifoldEdgesOff();
pEdges->Update();
vtkPolyData * poly = pEdges->GetOutput();
// pEdges->ColoringOff();
// // pEdges->GetOutput()->BuildCells();
//
// std::cout << "V1" << std::endl;
// std::cout << pEdges->GetOutput()->GetNumberOfCells() << std::endl;
// std::cout << pEdges->GetOutput()->GetNumberOfLines() << std::endl;
// std::cout << pEdges->GetOutput()->GetNumberOfPieces() << std::endl;
// std::cout << pEdges->GetOutput()->GetNumberOfPolys() << std::endl;
// std::cout << pEdges->GetOutput()->GetNumberOfStrips() << std::endl;
// std::cout << pEdges->GetOutput()->GetNumberOfVerts() << std::endl;
// std::cout << pEdges->GetOutput()->GetNumberOfPoints() << std::endl;
// // std::cout << pEdges->GetOutput()->GetNumberOfElements() << std::endl;
//
// // pEdges->GetOutput()->GetLines()->GetCell(0)->Print( std::cout );
//
// // pEdges->GetOutput()->BuildCells();
// TEUCHOS_ASSERT_EQUALITY( 0, pEdges->GetErrorCode() );
//
// std::cout << "W-1" << std::endl;
// int numLines = poly->GetNumberOfLines();
// vtkIdType * pts;
// // vtkIdList * pts2;
// for ( vtkIdType lineId=0; lineId<numLines; lineId++ )
// {
// vtkIdType numPoints;
// pEdges->GetOutput()->GetLines()->GetCell( lineId, numPoints, pts );
// // pEdges->GetOutput()->GetCellPoints( cellId, pts2 );
//
// if ( numPoints!=2 )
// {
// std::cout << "AAAAAAAAH!" << std::endl;
// continue;
// }
// // make sure we're dealing with an actual *edge* here.
// TEUCHOS_ASSERT_EQUALITY( numPoints, 2 );
// std::cout << pts[0] << " " << pts[1] << std::endl;
// }
// std::cout << "W0" << std::endl;
// poly->GetLines()->Print( std::cout );
//
// std::cout << "W1" << std::endl;
// poly->GetPoints()->Print( std::cout );
//
// std::cout << "W2" << std::endl;
double x[3];
// Teuchos::ArrayRCP<bool> boundaryPoints( numPoints, false );
Teuchos::ArrayRCP<bool> isBoundaryNodes( numPoints );
for ( int k=0; k<poly->GetNumberOfPoints(); k++ )
{
poly->GetPoint( k, x );
vtkIdType ptId = vtkMesh->FindPoint( x );
isBoundaryNodes[ ptId ] = true;
}
mesh->setBoundaryNodes( isBoundaryNodes );
// for ( int k=0; k<boundaryPoints.size(); k++ )
// std::cout << boundaryPoints[k] << std::endl;
// std::cout << "WWW" << std::endl;
// poly->Print( std::cout );
// vtkCellArray * verts = poly->GetVerts();
// verts->Print( std::cout );
// std::cout << "XXX" << std::endl;
// poly->GetData()->Print( std::cout );
// int numBoundaryPoints = poly->GetNumberOfPoints();
// Teuchos::ArrayRCP<Teuchos::Tuple<double,3> > boundaryPoints( numBoundaryPoints );
// for ( unsigned int k=0; k<numBoundaryPoints; k++ )
// poly->GetPoint( k, boundaryPoints[k].getRawPtr() );
// mesh->setBoundaryNodes( boundaryPoints );
// for ( int k=0; k<points.size(); k++ )
// std::cout << boundaryPoints[k] << std::endl;
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// get cells
int globalNumElems = vtkMesh->GetNumberOfCells();
// create an appropriate map
Teuchos::RCP<const Epetra_Map> elemsMap =
Teuchos::rcp ( new Epetra_Map ( globalNumElems, 0, *comm ) );
int localNumElems = elemsMap->NumMyElements();
Teuchos::ArrayRCP<Teuchos::ArrayRCP<int> > elems( localNumElems );
Teuchos::ArrayRCP<Mesh::ElementType> elemTypes( localNumElems );
for ( unsigned int k=0; k<localNumElems; k++ )
{
// set the connectivity table
vtkCell * cell = vtkMesh->GetCell( elemsMap->GID(k) );
int numPoints = cell->GetNumberOfPoints();
elems[k] = Teuchos::ArrayRCP<int>( numPoints );
for ( unsigned int l=0; l<numPoints; l++ )
elems[k][l] = cell->GetPointId( l );
// set the element type
switch( cell->GetCellType() )
{
case VTK_LINE:
elemTypes[k] = Mesh::EDGE2;
break;
case VTK_QUADRATIC_EDGE:
elemTypes[k] = Mesh::EDGE3;
break;
case VTK_TRIANGLE:
elemTypes[k] = Mesh::TRI3;
break;
case VTK_QUADRATIC_TRIANGLE:
elemTypes[k] = Mesh::TRI6;
break;
case VTK_QUAD:
elemTypes[k] = Mesh::QUAD4;
break;
case VTK_QUADRATIC_QUAD:
elemTypes[k] = Mesh::QUAD8;
break;
case VTK_BIQUADRATIC_QUAD:
elemTypes[k] = Mesh::QUAD9;
break;
case VTK_TETRA:
elemTypes[k] = Mesh::TET4;
break;
case VTK_QUADRATIC_TETRA:
elemTypes[k] = Mesh::TET10;
break;
case VTK_HEXAHEDRON:
elemTypes[k] = Mesh::HEX8;
break;
case VTK_QUADRATIC_HEXAHEDRON:
elemTypes[k] = Mesh::HEX20;
break;
case VTK_WEDGE:
elemTypes[k] = Mesh::PRISM6;
break;
case VTK_HIGHER_ORDER_WEDGE:
elemTypes[k] = Mesh::PRISM15;
break;
case VTK_PYRAMID:
elemTypes[k] = Mesh::PYRAMID5;
break;
default:
TEST_FOR_EXCEPTION( true,
std::logic_error,
"Unknown type \""<< cell->GetCellType() <<"\"." );
}
}
mesh->setElems( elems );
mesh->setElemTypes( elemTypes );
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
return mesh;
}