void writeToScreen(std::ostream & os,const Thyra::VectorBase<double> & src)
{
const Thyra::SpmdVectorBase<double> & spmdSrc =
Teuchos::dyn_cast<const Thyra::SpmdVectorBase<double> >(src);
// get access to data
Teuchos::ArrayRCP<const double> srcData;
spmdSrc.getLocalData(Teuchos::ptrFromRef(srcData));
os << "Local Size = " << srcData.size() << std::endl;
for (int i=0; i < srcData.size(); ++i) {
os << " " << srcData[i] << std::endl;
}
}
void LocalAggregationAlgorithm<LocalOrdinal, GlobalOrdinal, Node, LocalMatOps>::RandomReorder(Teuchos::ArrayRCP<LO> list) const {
//TODO: replace int
int n = list.size();
for(int i=0; i<n-1; i++) {
std::swap(list[i], list[RandomOrdinal(i,n-1)]);
}
}
//------------------------------------------------------------------------------
void
Albany::MechanicsProblem::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct>> meshSpecs,
Albany::StateManager& stateMgr)
{
// Construct All Phalanx Evaluators
int physSets = meshSpecs.size();
*out << "Num MeshSpecs: " << physSets << '\n';
fm.resize(physSets);
bool haveSidesets = false;
*out << "Calling MechanicsProblem::buildEvaluators" << '\n';
for (int ps = 0; ps < physSets; ++ps) {
fm[ps] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[ps], *meshSpecs[ps], stateMgr, BUILD_RESID_FM,
Teuchos::null);
if (meshSpecs[ps]->ssNames.size() > 0) haveSidesets = true;
}
constructDirichletEvaluators(*meshSpecs[0]);
if (haveSidesets)
constructNeumannEvaluators(meshSpecs[0]);
}
void Hydrology::buildProblem (Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
// Building cell basis and cubature
const CellTopologyData * const cell_top = &meshSpecs[0]->ctd;
intrepidBasis = Albany::getIntrepid2Basis(*cell_top);
cellType = Teuchos::rcp(new shards::CellTopology (cell_top));
Intrepid2::DefaultCubatureFactory cubFactory;
cubature = cubFactory.create<PHX::Device, RealType, RealType>(*cellType, meshSpecs[0]->cubatureDegree);
elementBlockName = meshSpecs[0]->ebName;
const int worksetSize = meshSpecs[0]->worksetSize;
const int numCellVertices = cellType->getNodeCount();
const int numCellNodes = intrepidBasis->getCardinality();
const int numCellQPs = cubature->getNumPoints();
dl = Teuchos::rcp(new Albany::Layouts(worksetSize,numCellVertices,numCellNodes,numCellQPs,numDim));
/* Construct All Phalanx Evaluators */
TEUCHOS_TEST_FOR_EXCEPTION(meshSpecs.size()!=1,std::logic_error,"Problem supports one Material Block");
fm.resize(1);
fm[0] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[0], *meshSpecs[0], stateMgr, Albany::BUILD_RESID_FM,Teuchos::null);
if(meshSpecs[0]->nsNames.size() > 0) {
// Build a nodeset evaluator if nodesets are present
constructDirichletEvaluators(*meshSpecs[0]);
}
if(meshSpecs[0]->ssNames.size() > 0) {
// Build a sideset evaluator if sidesets are present
constructNeumannEvaluators(meshSpecs[0]);
}
}
void IntrepidKernel<Scalar>::evaluate(
Teuchos::ArrayRCP<Scalar> &function_values,
const Teuchos::ArrayRCP<Scalar> &coeffs,
const Teuchos::ArrayRCP<Scalar> &dfunc_values )
{
int dim1 = this->b_cardinality;
testPrecondition( dim1 == (int) coeffs.size(),
"Function coefficients size does not match basis cardinality" );
MDArray function_coeffs( 1, dim1 );
for ( int m = 0; m < dim1; ++m )
{
function_coeffs(0,m) = coeffs[m];
}
MDArray basis_eval( 1, dim1, 1 );
for ( int i = 0; i < dim1; ++i )
{
basis_eval( 0, i, 0 ) = dfunc_values[i];
}
Teuchos::Tuple<int,2> function_dimensions;
function_dimensions[0] = 1;
function_dimensions[1] = 1;
MDArray function_eval( function_dimensions, function_values );
Intrepid::FunctionSpaceTools::evaluate<Scalar>( function_eval,
function_coeffs,
basis_eval );
}
void
Albany::PNPProblem::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
using Teuchos::rcp;
/* Construct All Phalanx Evaluators */
int physSets = meshSpecs.size();
std::cout << "PNP Problem Num MeshSpecs: " << physSets << std::endl;
fm.resize(physSets);
for (int ps=0; ps<physSets; ps++) {
fm[ps] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[ps], *meshSpecs[ps], stateMgr, BUILD_RESID_FM,
Teuchos::null);
}
if(meshSpecs[0]->nsNames.size() > 0) // Build a nodeset evaluator if nodesets are present
constructDirichletEvaluators(*meshSpecs[0]);
if(meshSpecs[0]->ssNames.size() > 0) // Build a sideset evaluator if sidesets are present
constructNeumannEvaluators(meshSpecs[0]);
}
void
Albany::NavierStokes::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
using Teuchos::rcp;
/* Construct All Phalanx Evaluators */
TEUCHOS_TEST_FOR_EXCEPTION(meshSpecs.size()!=1,std::logic_error,"Problem supports one Material Block");
fm.resize(1);
fm[0] = rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[0], *meshSpecs[0], stateMgr, BUILD_RESID_FM,
Teuchos::null);
if(meshSpecs[0]->nsNames.size() > 0) // Build a nodeset evaluator if nodesets are present
constructDirichletEvaluators(meshSpecs[0]->nsNames);
if(meshSpecs[0]->ssNames.size() > 0) // Build a sideset evaluator if sidesets are present
constructNeumannEvaluators(meshSpecs[0]);
}
void
Albany::HMCProblem::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct>> meshSpecs,
Albany::StateManager& stateMgr)
{
/* Construct All Phalanx Evaluators */
TEUCHOS_TEST_FOR_EXCEPTION(meshSpecs.size()!=1,std::logic_error,"Problem supports one Material Block");
fm.resize(1);
fm[0] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[0], *meshSpecs[0], stateMgr, BUILD_RESID_FM,
Teuchos::null);
if(meshSpecs[0]->nsNames.size() > 0) // Build a nodeset evaluator if nodesets are present
constructDirichletEvaluators(*meshSpecs[0]);
if(meshSpecs[0]->ssNames.size() > 0) // Build a sideset evaluator if sidesets are present
constructNeumannEvaluators(meshSpecs[0]);
#ifdef ALBANY_ATO
if( params->isType<Teuchos::RCP<ATO::Topology>>("Topology") )
setupTopOpt(meshSpecs,stateMgr);
#endif
}
DataTransferKit::FieldContainer<double>
MultiAppDTKUserObjectEvaluator::evaluate(const Teuchos::ArrayRCP<GlobalOrdinal>& bids, const Teuchos::ArrayRCP<double>& coords)
{
Teuchos::RCP<const Teuchos::Comm<int> > comm = Teuchos::rcp(new Teuchos::MpiComm<int>(Teuchos::rcp(new Teuchos::OpaqueWrapper<MPI_Comm>(libMesh::COMM_WORLD))));
int num_values = bids.size();
Teuchos::ArrayRCP<double> evaluated_data(num_values);
unsigned int dim = 3; // TODO: REPLACE ME!!!!!!!!!
for (GlobalOrdinal i=0; i<num_values; i++)
{
// See if this app is on this processor
if (std::binary_search(_box_ids.begin(), _box_ids.end(), bids[i]))
{
GlobalOrdinal app = bids[i];
Point p;
for(unsigned int j=0; j<dim; j++)
p(j) = coords[(j*num_values)+i];
evaluated_data[i] = _multi_app.appUserObjectBase(app, _user_object_name).spatialValue(p);
}
else
evaluated_data[i] = 0.0;
}
return DataTransferKit::FieldContainer<double>(evaluated_data, 1);
}
void
Albany::PoissonsEquationProblem::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
int physSets = meshSpecs.size();
*out << "Num MeshSpecs: " << physSets << '\n';
fm.resize(physSets);
bool haveSidesets = false;
*out << "Calling PoissonsEquationProblem::buildEvaluators" << '\n';
for (int ps = 0; ps < physSets; ++ps) {
fm[ps] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[ps], *meshSpecs[ps], stateMgr, BUILD_RESID_FM,
Teuchos::null);
if (meshSpecs[ps]->ssNames.size() > 0) haveSidesets = true;
}
constructDirichletEvaluators(*meshSpecs[0]);
if( haveSidesets )
constructNeumannEvaluators(meshSpecs[0]);
if( params->isType<Teuchos::RCP<ATO::Topology> >("Topology") )
setupTopOpt(meshSpecs,stateMgr);
}
MyField evaluate(
const Teuchos::ArrayRCP<MyMesh::global_ordinal_type>& elements,
const Teuchos::ArrayRCP<double>& coords )
{
int num_elements = elements.size();
MyField evaluated_data( num_elements, 3 );
for ( int n = 0; n < num_elements; ++n )
{
if ( std::find( d_mesh.elementsBegin(),
d_mesh.elementsEnd(),
elements[n] ) != d_mesh.elementsEnd() )
{
*(evaluated_data.begin() + n ) = d_comm->getRank() + 1.0;
*(evaluated_data.begin() + num_elements + n ) =
d_comm->getRank() + 1.0;
*(evaluated_data.begin() + 2*num_elements + n ) =
d_comm->getRank() + 1.0;
}
else
{
*(evaluated_data.begin() + n ) = 0.0;
*(evaluated_data.begin() + num_elements + n ) = 0.0;
*(evaluated_data.begin() + 2*num_elements + n ) = 0.0;
}
}
return evaluated_data;
}
//-----------------------------------------------------------------------------
void TpetraVector::set_local(const std::vector<double>& values)
{
dolfin_assert(!_x.is_null());
const std::size_t num_values = local_size();
if (values.size() != num_values)
{
dolfin_error("TpetraVector.cpp",
"set local values of Tpetra vector",
"Size of values array is not equal to local vector size");
}
if (num_values == 0)
return;
Teuchos::ArrayRCP<double> arr = _x->getDataNonConst(0);
std::copy(values.begin(), values.end(), arr.get());
}
void
Filtered_UniqueGlobalIndexer<LocalOrdinalT,GlobalOrdinalT>::
getOwnedAndGhostedNotFilteredIndicator(std::vector<int> & indicator) const
{
using Teuchos::RCP;
typedef GlobalOrdinalT GO;
typedef LocalOrdinalT LO;
typedef panzer::TpetraNodeType Node;
typedef Tpetra::Map<LO, GO, Node> Map;
typedef Tpetra::Vector<GO,LO,GO,Node> Vector;
typedef Tpetra::Import<LO,GO,Node> Import;
std::vector<GlobalOrdinalT> ownedIndices;
std::vector<GlobalOrdinalT> ghostedIndices;
// build owned and ghosted maps
getOwnedIndices(ownedIndices);
getOwnedAndGhostedIndices(ghostedIndices);
RCP<const Map> ownedMap
= Tpetra::createNonContigMap<LO,GO>(ownedIndices,getComm());
RCP<const Map> ghostedMap
= Tpetra::createNonContigMap<LO,GO>(ghostedIndices,getComm());
// allocate the owned vector, mark those GIDs as unfiltered
// (they are by definition)
Vector ownedActive(ownedMap);
ownedActive.putScalar(1);
// Initialize all indices to zero
Vector ghostedActive(ghostedMap);
ghostedActive.putScalar(0);
// do communication, marking unfiltered indices as 1 (filtered
// indices locally are marked as zero)
Import importer(ownedMap,ghostedMap);
ghostedActive.doImport(ownedActive,importer,Tpetra::INSERT);
Teuchos::ArrayRCP<const GO> data = ghostedActive.getData();
// copy communicated data (clear it out first)
indicator.clear();
indicator.insert(indicator.end(),data.begin(),data.end());
}
DataTransferKit::FieldContainer<double> evaluate(
const Teuchos::ArrayRCP<int>& gids,
const Teuchos::ArrayRCP<double>& coords )
{
Teuchos::ArrayRCP<double> evaluated_data( gids.size() );
for ( int n = 0; n < gids.size(); ++n )
{
if ( std::find( d_geom_gids.begin(),
d_geom_gids.end(),
gids[n] ) != d_geom_gids.end() )
{
evaluated_data[n] = 1.0 + gids[n];
}
else
{
evaluated_data[n] = 0.0;
}
}
return DataTransferKit::FieldContainer<double>( evaluated_data, 1 );
}
MyField evaluate(
const Teuchos::ArrayRCP<int>& gids,
const Teuchos::ArrayRCP<double>& coords )
{
MyField evaluated_data( gids.size(), 1 );
for ( int n = 0; n < gids.size(); ++n )
{
if ( std::find( d_geom_gids.begin(),
d_geom_gids.end(),
gids[n] ) != d_geom_gids.end() )
{
*(evaluated_data.begin() + n ) = 1.0;
}
else
{
*(evaluated_data.begin() + n ) = 0.0;
}
}
return evaluated_data;
}
MyField evaluate(
const Teuchos::ArrayRCP<
DataTransferKit::MeshContainer<int>::global_ordinal_type>& elements,
const Teuchos::ArrayRCP<double>& coords )
{
MyField evaluated_data( elements.size(), 1 );
for ( int n = 0; n < elements.size(); ++n )
{
if ( std::find( d_mesh.elementsBegin(),
d_mesh.elementsEnd(),
elements[n] ) != d_mesh.elementsEnd() )
{
*(evaluated_data.begin() + n ) = d_comm->getRank() + 1.0;
}
else
{
*(evaluated_data.begin() + n ) = 0.0;
}
}
return evaluated_data;
}
void Ifpack2Smoother<Scalar, LocalOrdinal, GlobalOrdinal, Node>::SetupLineSmoothing(Level& currentLevel) {
if (this->IsSetup() == true)
this->GetOStream(Warnings0) << "MueLu::Ifpack2Smoother::Setup(): Setup() has already been called" << std::endl;
ParameterList& myparamList = const_cast<ParameterList&>(this->GetParameterList());
LO CoarseNumZLayers = Factory::Get<LO>(currentLevel,"CoarseNumZLayers");
if (CoarseNumZLayers > 0) {
Teuchos::ArrayRCP<LO> TVertLineIdSmoo = Factory::Get< Teuchos::ArrayRCP<LO> >(currentLevel, "LineDetection_VertLineIds");
// determine number of local parts
LO maxPart = 0;
for(size_t k = 0; k < Teuchos::as<size_t>(TVertLineIdSmoo.size()); k++) {
if(maxPart < TVertLineIdSmoo[k]) maxPart = TVertLineIdSmoo[k];
}
size_t numLocalRows = A_->getNodeNumRows();
TEUCHOS_TEST_FOR_EXCEPTION(numLocalRows % TVertLineIdSmoo.size() != 0, Exceptions::RuntimeError,
"MueLu::Ifpack2Smoother::Setup(): the number of local nodes is incompatible with the TVertLineIdsSmoo.");
if (numLocalRows == Teuchos::as<size_t>(TVertLineIdSmoo.size())) {
myparamList.set("partitioner: type","user");
myparamList.set("partitioner: map",TVertLineIdSmoo);
myparamList.set("partitioner: local parts",maxPart+1);
} else {
// we assume a constant number of DOFs per node
size_t numDofsPerNode = numLocalRows / TVertLineIdSmoo.size();
// Create a new Teuchos::ArrayRCP<LO> of size numLocalRows and fill it with the corresponding information
Teuchos::ArrayRCP<LO> partitionerMap(numLocalRows, Teuchos::OrdinalTraits<LocalOrdinal>::invalid());
for (size_t blockRow = 0; blockRow < Teuchos::as<size_t>(TVertLineIdSmoo.size()); ++blockRow)
for (size_t dof = 0; dof < numDofsPerNode; dof++)
partitionerMap[blockRow * numDofsPerNode + dof] = TVertLineIdSmoo[blockRow];
myparamList.set("partitioner: type","user");
myparamList.set("partitioner: map",partitionerMap);
myparamList.set("partitioner: local parts",maxPart + 1);
}
if (type_ == "LINESMOOTHING_BANDED_RELAXATION" ||
type_ == "LINESMOOTHING_BANDED RELAXATION" ||
type_ == "LINESMOOTHING_BANDEDRELAXATION")
type_ = "BANDEDRELAXATION";
else
type_ = "BLOCKRELAXATION";
} else {
// line detection failed -> fallback to point-wise relaxation
this->GetOStream(Runtime0) << "Line detection failed: fall back to point-wise relaxation" << std::endl;
myparamList.remove("partitioner: type",false);
myparamList.remove("partitioner: map", false);
myparamList.remove("partitioner: local parts",false);
type_ = "RELAXATION";
}
RCP<const Tpetra::RowMatrix<SC, LO, GO, NO> > tpA = Utilities::Op2NonConstTpetraRow(A_);
prec_ = Ifpack2::Factory::create(type_, tpA, overlap_);
SetPrecParameters();
prec_->initialize();
prec_->compute();
}
//-----------------------------------------------------------------------------
void TpetraVector::gather_on_zero(std::vector<double>& v) const
{
dolfin_assert(!_x.is_null());
if (_x->getMap()->getComm()->getRank() == 0)
v.resize(size());
else
v.resize(0);
// Create map with elements only on process zero
Teuchos::RCP<map_type> ymap(new map_type(size(), v.size(), 0,
_x->getMap()->getComm()));
Teuchos::RCP<vector_type> y(new vector_type(ymap, 1));
// Export from vector x to vector y
Tpetra::Export<vector_type::local_ordinal_type,
vector_type::global_ordinal_type,
vector_type::node_type> exporter(_x->getMap(), ymap);
y->doExport(*_x, exporter, Tpetra::INSERT);
Teuchos::ArrayRCP<const double> yarr = y->getData(0);
std::copy(yarr.get(), yarr.get() + v.size(), v.begin());
}
LCM::
Schwarz_BoundaryJacobian::
Schwarz_BoundaryJacobian(
Teuchos::RCP<Teuchos_Comm const> const & comm,
Teuchos::ArrayRCP<Teuchos::RCP<Albany::Application>> const & ca,
Teuchos::Array<Teuchos::RCP<Tpetra_CrsMatrix>> jacs,
int const this_app_index,
int const coupled_app_index) :
commT_(comm),
coupled_apps_(ca),
jacs_(jacs),
this_app_index_(this_app_index),
coupled_app_index_(coupled_app_index),
b_use_transpose_(false),
b_initialized_(false),
n_models_(0)
{
assert(0 <= this_app_index && this_app_index < ca.size());
assert(0 <= coupled_app_index && coupled_app_index < ca.size());
domain_map_ = ca[coupled_app_index]->getMapT();
range_map_ = ca[this_app_index]->getMapT();
}
void
Albany::Helmholtz2DProblem::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
/* Construct All Phalanx Evaluators */
TEUCHOS_TEST_FOR_EXCEPTION(meshSpecs.size()!=1,std::logic_error,"Problem supports one Material Block");
fm.resize(1);
fm[0] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[0], *meshSpecs[0], stateMgr, BUILD_RESID_FM,
Teuchos::null);
constructDirichletEvaluators(*meshSpecs[0]);
}
//! Copy a flat vector into a product vector
void copyFlatThyraIntoBlockedThyra(const Thyra::VectorBase<double>& src,
const Teuchos::Ptr<Thyra::VectorBase<double> > & dest) const
{
using Teuchos::RCP;
using Teuchos::ArrayView;
using Teuchos::rcpFromPtr;
using Teuchos::rcp_dynamic_cast;
const RCP<Thyra::ProductVectorBase<double> > prodDest =
Thyra::castOrCreateNonconstProductVectorBase(rcpFromPtr(dest));
const Thyra::SpmdVectorBase<double> & spmdSrc =
Teuchos::dyn_cast<const Thyra::SpmdVectorBase<double> >(src);
// get access to flat data
Teuchos::ArrayRCP<const double> srcData;
spmdSrc.getLocalData(Teuchos::ptrFromRef(srcData));
std::size_t offset = 0;
const int numBlocks = prodDest->productSpace()->numBlocks();
for (int b = 0; b < numBlocks; ++b) {
const RCP<Thyra::VectorBase<double> > destBlk = prodDest->getNonconstVectorBlock(b);
// get access to blocked data
const RCP<Thyra::SpmdVectorBase<double> > spmdBlk =
rcp_dynamic_cast<Thyra::SpmdVectorBase<double> >(destBlk, true);
Teuchos::ArrayRCP<double> destData;
spmdBlk->getNonconstLocalData(Teuchos::ptrFromRef(destData));
// perform copy
for (int i=0; i < destData.size(); ++i) {
destData[i] = srcData[i+offset];
}
offset += destData.size();
}
}
void
Aeras::ShallowWaterProblemNoAD::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
using Teuchos::rcp;
/* Construct All Phalanx Evaluators */
TEUCHOS_TEST_FOR_EXCEPTION(meshSpecs.size()!=1,std::logic_error,"Problem supports one Material Block");
fm.resize(1);
fm[0] = rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[0], *meshSpecs[0], stateMgr, Albany::BUILD_RESID_FM,
Teuchos::null);
}
void
Albany::PeridigmProblem::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct>> meshSpecs,
Albany::StateManager& stateMgr)
{
/* Construct All Phalanx Evaluators */
int physSets = meshSpecs.size();
fm.resize(physSets);
for (int ps=0; ps<physSets; ps++) {
fm[ps] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[ps], *meshSpecs[ps], stateMgr, BUILD_RESID_FM, Teuchos::null);
}
constructDirichletEvaluators(*meshSpecs[0]);
}
void
FELIX::StokesL1L2::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
using Teuchos::rcp;
std::cout << "In StokesL1L2 Problem!" << std::endl;
/* Construct All Phalanx Evaluators */
TEUCHOS_TEST_FOR_EXCEPTION(meshSpecs.size()!=1,std::logic_error,"Problem supports one Material Block");
fm.resize(1);
fm[0] = rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[0], *meshSpecs[0], stateMgr, Albany::BUILD_RESID_FM,
Teuchos::null);
constructDirichletEvaluators(*meshSpecs[0]);
}
void
Tsunami::Boussinesq::
buildProblem(
Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
using Teuchos::rcp;
/* Construct All Phalanx Evaluators */
TEUCHOS_TEST_FOR_EXCEPTION(meshSpecs.size()!=1,std::logic_error,"Problem supports one Material Block");
fm.resize(1);
fm[0] = rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
elementBlockName = meshSpecs[0]->ebName;
buildEvaluators(*fm[0], *meshSpecs[0], stateMgr, Albany::BUILD_RESID_FM,
Teuchos::null);
constructDirichletEvaluators(*meshSpecs[0]);
//construct Neumann evaluators
constructNeumannEvaluators(meshSpecs[0]);
}
Teuchos::RCP<const Teuchos::ParameterList>
getValidInitialConditionParameters(const Teuchos::ArrayRCP<std::string>& wsEBNames) {
Teuchos::RCP<Teuchos::ParameterList> validPL =
rcp(new Teuchos::ParameterList("ValidInitialConditionParams"));;
validPL->set<std::string>("Function", "", "");
Teuchos::Array<double> defaultData;
validPL->set<Teuchos::Array<double> >("Function Data", defaultData, "");
// Validate element block constant data
for(int i = 0; i < wsEBNames.size(); i++)
validPL->set<Teuchos::Array<double> >(wsEBNames[i], defaultData, "");
// For EBConstant data, we can optionally randomly perturb the IC on each variable some amount
validPL->set<Teuchos::Array<double> >("Perturb IC", defaultData, "");
return validPL;
}
//------------------------------------------------------------------------------
void
Albany::ConcurrentMultiscaleProblem::
buildProblem(Teuchos::ArrayRCP<Teuchos::RCP<Albany::MeshSpecsStruct> > meshSpecs,
Albany::StateManager& stateMgr)
{
// Construct All Phalanx Evaluators
int physSets = meshSpecs.size();
std::cout << "Num MeshSpecs: " << physSets << std::endl;
fm.resize(physSets);
std::cout << "Calling ConcurrentMultiscaleProblem::buildEvaluators" << std::endl;
for (int ps=0; ps < physSets; ++ps) {
std::string eb_name = meshSpecs[ps]->ebName;
if ( material_db_->isElementBlockParam(eb_name,"Lagrange Multiplier Block") ) {
lm_overlap_map_.insert(std::make_pair(eb_name,
material_db_->getElementBlockParam<bool>(eb_name,"Lagrange Multiplier Block") ) );
}
if ( material_db_->isElementBlockParam(eb_name,"Coarse Overlap Block") ) {
coarse_overlap_map_.insert(std::make_pair(eb_name,
material_db_->getElementBlockParam<bool>(eb_name,"Coarse Overlap Block") ) );
}
if ( material_db_->isElementBlockParam(eb_name,"Fine Overlap Block") ) {
fine_overlap_map_.insert(std::make_pair(eb_name,
material_db_->getElementBlockParam<bool>(eb_name,"Fine Overlap Block") ) );
}
fm[ps] = Teuchos::rcp(new PHX::FieldManager<PHAL::AlbanyTraits>);
buildEvaluators(*fm[ps], *meshSpecs[ps], stateMgr, BUILD_RESID_FM,
Teuchos::null);
}
constructDirichletEvaluators(*meshSpecs[0]);
}
void DiscreteBoundaryOperator<ValueType>::applyImpl(
const Thyra::EOpTransp M_trans,
const Thyra::MultiVectorBase<ValueType> &X_in,
const Teuchos::Ptr<Thyra::MultiVectorBase<ValueType>> &Y_inout,
const ValueType alpha, const ValueType beta) const {
typedef Thyra::Ordinal Ordinal;
// Note: the name is VERY misleading: these asserts don't disappear in
// release runs, and in case of failure throw exceptions rather than
// abort.
TEUCHOS_ASSERT(this->opSupported(M_trans));
TEUCHOS_ASSERT(X_in.range()->isCompatible(*this->domain()));
TEUCHOS_ASSERT(Y_inout->range()->isCompatible(*this->range()));
TEUCHOS_ASSERT(Y_inout->domain()->isCompatible(*X_in.domain()));
const Ordinal colCount = X_in.domain()->dim();
// Loop over the input columns
for (Ordinal col = 0; col < colCount; ++col) {
// Get access the the elements of X_in's and Y_inout's column #col
Thyra::ConstDetachedSpmdVectorView<ValueType> xVec(X_in.col(col));
Thyra::DetachedSpmdVectorView<ValueType> yVec(Y_inout->col(col));
const Teuchos::ArrayRCP<const ValueType> xArray(xVec.sv().values());
const Teuchos::ArrayRCP<ValueType> yArray(yVec.sv().values());
// Wrap the Trilinos array in an Armadillo vector. const_cast is used
// because it's more natural to have a const arma::Col<ValueType> array
// than an arma::Col<const ValueType> one.
const arma::Col<ValueType> xCol(const_cast<ValueType *>(xArray.get()),
xArray.size(), false /* copy_aux_mem */);
arma::Col<ValueType> yCol(yArray.get(), yArray.size(), false);
applyBuiltInImpl(static_cast<TranspositionMode>(M_trans), xCol, yCol, alpha,
beta);
}
}
int main_(Teuchos::CommandLineProcessor &clp, int argc, char *argv[]) {
#include <MueLu_UseShortNames.hpp>
using Teuchos::RCP;
using Teuchos::rcp;
using Teuchos::TimeMonitor;
// =========================================================================
// MPI initialization using Teuchos
// =========================================================================
Teuchos::GlobalMPISession mpiSession(&argc, &argv, NULL);
RCP< const Teuchos::Comm<int> > comm = Teuchos::DefaultComm<int>::getComm();
int numProc = comm->getSize();
int myRank = comm->getRank();
// =========================================================================
// Parameters initialization
// =========================================================================
::Xpetra::Parameters xpetraParameters(clp);
bool runHeavyTests = false;
clp.setOption("heavytests", "noheavytests", &runHeavyTests, "whether to exercise tests that take a long time to run");
clp.recogniseAllOptions(true);
switch (clp.parse(argc,argv)) {
case Teuchos::CommandLineProcessor::PARSE_HELP_PRINTED: return EXIT_SUCCESS;
case Teuchos::CommandLineProcessor::PARSE_ERROR:
case Teuchos::CommandLineProcessor::PARSE_UNRECOGNIZED_OPTION: return EXIT_FAILURE;
case Teuchos::CommandLineProcessor::PARSE_SUCCESSFUL: break;
}
Xpetra::UnderlyingLib lib = xpetraParameters.GetLib();
// =========================================================================
// Problem construction
// =========================================================================
ParameterList matrixParameters;
matrixParameters.set("nx", Teuchos::as<GO>(9999));
matrixParameters.set("matrixType", "Laplace1D");
RCP<Matrix> A = MueLuTests::TestHelpers::TestFactory<SC, LO, GO, NO>::Build1DPoisson(matrixParameters.get<GO>("nx"), lib);
RCP<MultiVector> coordinates = Galeri::Xpetra::Utils::CreateCartesianCoordinates<SC,LO,GO,Map,MultiVector>("1D", A->getRowMap(), matrixParameters);
std::string outDir = "Output/";
std::vector<std::string> dirList;
if (runHeavyTests) {
dirList.push_back("EasyParameterListInterpreter-heavy/");
dirList.push_back("FactoryParameterListInterpreter-heavy/");
} else {
dirList.push_back("EasyParameterListInterpreter/");
dirList.push_back("FactoryParameterListInterpreter/");
}
#if defined(HAVE_MPI) && defined(HAVE_MUELU_ISORROPIA) && defined(HAVE_AMESOS2_KLU2)
// The ML interpreter have internal ifdef, which means that the resulting
// output would depend on configuration (reguarl interpreter does not have
// that). Therefore, we need to stabilize the configuration here.
// In addition, we run ML parameter list tests only if KLU is available
dirList.push_back("MLParameterListInterpreter/");
dirList.push_back("MLParameterListInterpreter2/");
#endif
int numLists = dirList.size();
bool failed = false;
Teuchos::Time timer("Interpreter timer");
//double lastTime = timer.wallTime();
for (int k = 0; k < numLists; k++) {
Teuchos::ArrayRCP<std::string> fileList = MueLuTests::TestHelpers::GetFileList(dirList[k],
(numProc == 1 ? std::string(".xml") : std::string("_np" + Teuchos::toString(numProc) + ".xml")));
for (int i = 0; i < fileList.size(); i++) {
// Set seed
std::srand(12345);
// Reset (potentially) cached value of the estimate
A->SetMaxEigenvalueEstimate(-Teuchos::ScalarTraits<SC>::one());
std::string xmlFile = dirList[k] + fileList[i];
std::string outFile = outDir + fileList[i];
std::string baseFile = outFile.substr(0, outFile.find_last_of('.'));
std::size_t found = baseFile.find("_np");
if (numProc == 1 && found != std::string::npos) {
#ifdef HAVE_MPI
baseFile = baseFile.substr(0, found);
#else
std::cout << "Skipping \"" << xmlFile << "\" as MPI is not enabled" << std::endl;
continue;
#endif
}
baseFile = baseFile + (lib == Xpetra::UseEpetra ? "_epetra" : "_tpetra");
std::string goldFile = baseFile + ".gold";
std::ifstream f(goldFile.c_str());
if (!f.good()) {
if (myRank == 0)
std::cout << "Warning: comparison file " << goldFile << " not found. Skipping test" << std::endl;
continue;
}
std::filebuf buffer;
std::streambuf* oldbuffer = NULL;
if (myRank == 0) {
// Redirect output
buffer.open((baseFile + ".out").c_str(), std::ios::out);
oldbuffer = std::cout.rdbuf(&buffer);
}
// NOTE: we cannot use ParameterListInterpreter(xmlFile, comm), because we want to update the ParameterList
// first to include "test" verbosity
Teuchos::ParameterList paramList;
Teuchos::updateParametersFromXmlFileAndBroadcast(xmlFile, Teuchos::Ptr<Teuchos::ParameterList>(¶mList), *comm);
if (dirList[k] == "EasyParameterListInterpreter/" || dirList[k] == "EasyParameterListInterpreter-heavy/")
paramList.set("verbosity", "test");
else if (dirList[k] == "FactoryParameterListInterpreter/" || dirList[k] == "FactoryParameterListInterpreter-heavy/")
paramList.sublist("Hierarchy").set("verbosity", "Test");
else if (dirList[k] == "MLParameterListInterpreter/")
paramList.set("ML output", 42);
else if (dirList[k] == "MLParameterListInterpreter2/")
paramList.set("ML output", 10);
try {
timer.start();
Teuchos::RCP<HierarchyManager> mueluFactory;
// create parameter list interpreter
// here we have to distinguish between the general MueLu parameter list interpreter
// and the ML parameter list interpreter. Note that the ML paramter interpreter also
// works with Tpetra matrices.
if (dirList[k] == "EasyParameterListInterpreter/" ||
dirList[k] == "EasyParameterListInterpreter-heavy/" ||
dirList[k] == "FactoryParameterListInterpreter/" ||
dirList[k] == "FactoryParameterListInterpreter-heavy/") {
mueluFactory = Teuchos::rcp(new ParameterListInterpreter(paramList));
} else if (dirList[k] == "MLParameterListInterpreter/") {
mueluFactory = Teuchos::rcp(new MLParameterListInterpreter(paramList));
} else if (dirList[k] == "MLParameterListInterpreter2/") {
//std::cout << "ML ParameterList: " << std::endl;
//std::cout << paramList << std::endl;
RCP<ParameterList> mueluParamList = Teuchos::getParametersFromXmlString(MueLu::ML2MueLuParameterTranslator::translate(paramList,"SA"));
//std::cout << "MueLu ParameterList: " << std::endl;
//std::cout << *mueluParamList << std::endl;
mueluFactory = Teuchos::rcp(new ParameterListInterpreter(*mueluParamList));
}
RCP<Hierarchy> H = mueluFactory->CreateHierarchy();
H->GetLevel(0)->template Set<RCP<Matrix> >("A", A);
if (dirList[k] == "MLParameterListInterpreter/") {
// MLParameterInterpreter needs the nullspace information if rebalancing is active!
// add default constant null space vector
RCP<MultiVector> nullspace = MultiVectorFactory::Build(A->getRowMap(), 1);
nullspace->putScalar(1.0);
H->GetLevel(0)->Set("Nullspace", nullspace);
}
H->GetLevel(0)->Set("Coordinates", coordinates);
mueluFactory->SetupHierarchy(*H);
if (strncmp(fileList[i].c_str(), "reuse", 5) == 0) {
// Build the Hierarchy the second time
// Should be faster if we actually do the reuse
A->SetMaxEigenvalueEstimate(-Teuchos::ScalarTraits<SC>::one());
mueluFactory->SetupHierarchy(*H);
}
timer.stop();
} catch (Teuchos::ExceptionBase& e) {
std::string msg = e.what();
msg = msg.substr(msg.find_last_of('\n')+1);
if (myRank == 0) {
std::cout << "Caught exception: " << msg << std::endl;
// Redirect output back
std::cout.rdbuf(oldbuffer);
buffer.close();
}
if (msg == "Zoltan interface is not available" ||
msg == "Zoltan2 interface is not available" ||
msg == "MueLu::FactoryFactory:BuildFactory(): Cannot create a Zoltan2Interface object: Zoltan2 is disabled: HAVE_MUELU_ZOLTAN2 && HAVE_MPI == false.") {
if (myRank == 0)
std::cout << xmlFile << ": skipped (missing library)" << std::endl;
continue;
}
}
std::string cmd;
if (myRank == 0) {
// Redirect output back
std::cout.rdbuf(oldbuffer);
buffer.close();
// Create a copy of outputs
cmd = "cp -f ";
system((cmd + baseFile + ".gold " + baseFile + ".gold_filtered").c_str());
system((cmd + baseFile + ".out " + baseFile + ".out_filtered").c_str());
// Tpetra produces different eigenvalues in Chebyshev due to using
// std::rand() for generating random vectors, which may be initialized
// using different seed, and may have different algorithm from one
// gcc version to another, or to anogther compiler (like clang)
// This leads to us always failing this test.
// NOTE1 : Epetra, on the other hand, rolls out its out random number
// generator, which always produces same results
// Ignore the value of "lambdaMax"
run_sed("'s/lambdaMax: [0-9]*.[0-9]*/lambdaMax = <ignored>/'", baseFile);
// Ignore the value of "lambdaMin"
run_sed("'s/lambdaMin: [0-9]*.[0-9]*/lambdaMin = <ignored>/'", baseFile);
// Ignore the value of "chebyshev: max eigenvalue"
// NOTE: we skip lines with default value ([default])
run_sed("'/[default]/! s/chebyshev: max eigenvalue = [0-9]*.[0-9]*/chebyshev: max eigenvalue = <ignored>/'", baseFile);
// Ignore the exact type of direct solver (it is selected semi-automatically
// depending on how Trilinos was configured
run_sed("'s/Amesos\\([2]*\\)Smoother{type = .*}/Amesos\\1Smoother{type = <ignored>}/'", baseFile);
run_sed("'s/SuperLU solver interface, direct solve/<Direct> solver interface/'", baseFile);
run_sed("'s/KLU2 solver interface/<Direct> solver interface/'", baseFile);
run_sed("'s/Basker solver interface/<Direct> solver interface/'", baseFile);
// Strip template args for some classes
std::vector<std::string> classes;
classes.push_back("Xpetra::Matrix");
classes.push_back("MueLu::Constraint");
classes.push_back("MueLu::SmootherPrototype");
for (size_t q = 0; q < classes.size(); q++)
run_sed("'s/" + classes[q] + "<.*>/" + classes[q] + "<ignored> >/'", baseFile);
#ifdef __APPLE__
// Some Macs print outs ptrs as 0x0 instead of 0, fix that
run_sed("'/RCP/ s/=0x0/=0/g'", baseFile);
#endif
// Run comparison (ignoring whitespaces)
cmd = "diff -u -w -I\"^\\s*$\" " + baseFile + ".gold_filtered " + baseFile + ".out_filtered";
int ret = system(cmd.c_str());
if (ret)
failed = true;
//std::ios_base::fmtflags ff(std::cout.flags());
//std::cout.precision(2);
//std::cout << xmlFile << " (" << std::setiosflags(std::ios::fixed)
// << timer.wallTime() - lastTime << " sec.) : " << (ret ? "failed" : "passed") << std::endl;
//lastTime = timer.wallTime();
//std::cout.flags(ff); // reset flags to whatever they were prior to printing time
std::cout << xmlFile << " : " << (ret ? "failed" : "passed") << std::endl;
}
}
}
if (myRank == 0)
std::cout << std::endl << "End Result: TEST " << (failed ? "FAILED" : "PASSED") << std::endl;
return (failed ? EXIT_FAILURE : EXIT_SUCCESS);
}
int testNormalizeMat(RCP<MatOrthoManager<ST,MV,OP> > OM, RCP<const MV> S)
{
typedef MultiVecTraits<double,MV> MVT;
typedef OperatorTraits<double,MV,OP> OPT;
typedef ScalarTraits<double> SCT;
typedef SCT::magnitudeType MT;
const ST ONE = SCT::one();
const MT ZERO = SCT::magnitude(SCT::zero());
const int sizeS = MVT::GetNumberVecs(*S);
int numerr = 0;
bool hasM = (OM->getOp() != null);
std::ostringstream sout;
//
// output tests:
// <S_out,S_out> = I
// S_in = S_out B
//
// we will loop over an integer specifying the test combinations
// the bit pattern for the different tests is listed in parenthesis
//
// for each of the following, we should test B
//
// if hasM:
// with and without MS (1)
//
// as hasM controls the upper level bits, we need only run test case 0 if hasM==false
// otherwise, we run test cases 0-1
//
int numtests;
RCP<MV> MS;
if (hasM) {
MS = MVT::Clone(*S,sizeS);
OPT::Apply(*(OM->getOp()),*S ,*MS);
numtests = 2;
}
else {
numtests = 1;
}
for (int t=0; t<numtests; t++) {
// pointers to simplify calls below
RCP<MV> lclMS;
if ( t & 1 ) {
lclMS = MS;
}
Teuchos::ArrayRCP<ST> Bdata = Teuchos::arcp<ST>(sizeS*sizeS);
RCP<SerialDenseMatrix<int,ST> > B = rcp( new SerialDenseMatrix<int,ST>(Teuchos::View,Bdata.getRawPtr(),sizeS,sizeS,sizeS) );
try {
// call routine
// test all outputs for correctness
// here is where the outputs go
RCP<MV> Scopy, MScopy;
int ret;
// copies of S,MS
Scopy = MVT::CloneCopy(*S);
if (lclMS != Teuchos::null) {
MScopy = MVT::CloneCopy(*lclMS);
}
// randomize this data, it should be overwritten
B->random();
// run test
ret = OM->normalizeMat(*Scopy,B,MScopy);
sout << "normalizeMat() returned rank " << ret << endl;
if (ret == 0) {
sout << " Cannot continue." << endl;
numerr++;
break;
}
// normalizeMat() is only required to return a
// basis of rank "ret"
// this is what we will test:
// the first "ret" columns in Scopy, MScopy
// the first "ret" rows in B
// get pointers to the parts that we want
if (ret < sizeS) {
vector<int> ind(ret);
for (int i=0; i<ret; i++) {
ind[i] = i;
}
Scopy = MVT::CloneViewNonConst(*Scopy,ind);
if (MScopy != null) {
MScopy = MVT::CloneViewNonConst(*MScopy,ind);
}
B = rcp( new SerialDenseMatrix<int,ST>(Teuchos::View,Bdata.getRawPtr(),ret,ret,sizeS) );
}
// test all outputs for correctness
// MS == M*S
if (MScopy != null) {
RCP<MV> tmp = MVT::Clone(*Scopy,ret);
OPT::Apply(*(OM->getOp()),*Scopy,*tmp);
MT err = MVDiff(*tmp,*MScopy);
if (err > TOL) {
sout << " vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv tolerance exceeded! test failed!" << endl;
numerr++;
}
sout << " " << t << "|| MS - M*S || : " << err << endl;
}
// S^T M S == I
{
MT err = OM->orthonormError(*Scopy);
if (err > TOL) {
sout << " vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv tolerance exceeded! test failed!" << endl;
numerr++;
}
sout << " || <S,S> - I || after : " << err << endl;
}
// S_in = S_out*B
{
RCP<MV> tmp = MVT::Clone(*S,sizeS);
MVT::MvTimesMatAddMv(ONE,*Scopy,*B,ZERO,*tmp);
MT err = MVDiff(*tmp,*S);
if (err > ATOL*TOL) {
sout << " vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv tolerance exceeded! test failed!" << endl;
numerr++;
}
sout << " " << t << "|| S_in - S_out*B || : " << err << endl;
}
}
catch (const OrthoError &e) {
sout << " ------------------------------------------- normalizeMat() threw exception" << endl;
sout << " Error: " << e.what() << endl;
numerr++;
}
} // test for
MsgType type = Warnings;
if (numerr>0) type = Errors;
MyOM->stream(type) << sout.str();
MyOM->stream(type) << endl;
return numerr;
}
