void performNodalMeshReduction(
stk::mesh::Part &samplePart,
stk::mesh::BulkData& bulkData)
{
const stk::mesh::EntityRank nodeEntityRank(0);
const stk::mesh::MetaData &metaData = stk::mesh::MetaData::get(bulkData);
std::vector<stk::mesh::Entity *> sampleNodes;
stk::mesh::get_selected_entities(samplePart, bulkData.buckets(nodeEntityRank), sampleNodes);
const stk::mesh::Selector locallyOwned = stk::mesh::MetaData::get(bulkData).locally_owned_part();
std::vector<stk::mesh::Entity *> relatedEntities;
typedef boost::indirect_iterator<std::vector<stk::mesh::Entity *>::const_iterator> EntityIterator;
for (EntityIterator it(sampleNodes.begin()), it_end(sampleNodes.end()); it != it_end; ++it) {
const stk::mesh::PairIterRelation relations = it->relations();
typedef stk::mesh::PairIterRelation::first_type RelationIterator;
for (RelationIterator rel_it = relations.first, rel_it_end = relations.second; rel_it != rel_it_end; ++rel_it) {
const Teuchos::Ptr<stk::mesh::Entity> relatedEntity(rel_it->entity());
if (Teuchos::nonnull(relatedEntity) && locallyOwned(*relatedEntity)) {
relatedEntities.push_back(relatedEntity.get());
}
}
}
std::sort(relatedEntities.begin(), relatedEntities.end(), stk::mesh::EntityLess());
relatedEntities.erase(
std::unique(relatedEntities.begin(), relatedEntities.end(), stk::mesh::EntityEqual()),
relatedEntities.end());
std::vector<stk::mesh::Entity *> sampleClosure;
stk::mesh::find_closure(bulkData, relatedEntities, sampleClosure);
// Keep only the closure, remove the rest, by decreasing entityRanks
{
const stk::mesh::Selector ownedOrShared = metaData.locally_owned_part() | metaData.globally_shared_part();
typedef boost::indirect_iterator<std::vector<stk::mesh::Entity *>::const_iterator> EntityIterator;
EntityIterator allKeepersEnd(sampleClosure.end());
const EntityIterator allKeepersBegin(sampleClosure.begin());
for (stk::mesh::EntityRank candidateRankCount = metaData.entity_rank_count(); candidateRankCount > 0; --candidateRankCount) {
const stk::mesh::EntityRank candidateRank = candidateRankCount - 1;
const EntityIterator keepersBegin = std::lower_bound(allKeepersBegin, allKeepersEnd,
stk::mesh::EntityKey(candidateRank, 0),
stk::mesh::EntityLess());
const EntityIterator keepersEnd = allKeepersEnd;
std::vector<stk::mesh::Entity *> candidates;
stk::mesh::get_selected_entities(ownedOrShared, bulkData.buckets(candidateRank), candidates);
{
BulkModification modification(bulkData);
std::set_difference(candidates.begin(), candidates.end(),
keepersBegin.base(), keepersEnd.base(),
EntityDestructor(modification),
stk::mesh::EntityLess());
}
allKeepersEnd = keepersBegin;
}
}
}
void initializePrec(
const PreconditionerFactoryBase<Scalar> &precFactory,
const Teuchos::RCP<const LinearOpBase<Scalar> > &fwdOp,
const Teuchos::Ptr<PreconditionerBase<Scalar> > &prec,
const ESupportSolveUse supportSolveUse = SUPPORT_SOLVE_UNSPECIFIED
)
{
precFactory.initializePrec(defaultLinearOpSource(fwdOp), prec.get(),
supportSolveUse);
}
void ObserverImpl::observeSolution (
double stamp, const Epetra_Vector& nonOverlappedSolution,
const Teuchos::Ptr<const Epetra_Vector>& nonOverlappedSolutionDot)
{
// If solution == "Steady" or "Continuation", we need to update the solution
// from the initial guess prior to writing it out, or we will not get the
// proper state of things like "Stress" in the Exodus file.
{
// Evaluate state field manager
if(nonOverlappedSolutionDot != Teuchos::null)
app_->evaluateStateFieldManager(stamp, nonOverlappedSolutionDot.get(),
NULL, nonOverlappedSolution);
else
app_->evaluateStateFieldManager(stamp, NULL, NULL, nonOverlappedSolution);
// Renames the New state as the Old state in preparation for the next step
app_->getStateMgr().updateStates();
#ifdef ALBANY_PERIDIGM
#if defined(ALBANY_EPETRA)
const Teuchos::RCP<LCM::PeridigmManager>&
peridigmManager = LCM::PeridigmManager::self();
if (Teuchos::nonnull(peridigmManager)) {
peridigmManager->writePeridigmSubModel(stamp);
peridigmManager->updateState();
}
#endif
#endif
}
//! update distributed parameters in the mesh
Teuchos::RCP<DistParamLib> distParamLib = app_->getDistParamLib();
distParamLib->scatter();
DistParamLib::const_iterator it;
Teuchos::RCP<const Epetra_Comm> comm = app_->getEpetraComm();
for(it = distParamLib->begin(); it != distParamLib->end(); ++it) {
app_->getDiscretization()->setFieldT(*it->second->overlapped_vector(), it->second->name(),
/*overlapped*/ true);
}
StatelessObserverImpl::observeSolution(stamp, nonOverlappedSolution,
nonOverlappedSolutionDot);
}
void
Piro::MatrixFreeLinearOp<Scalar>::applyImpl(
const Thyra::EOpTransp M_trans,
const Thyra::MultiVectorBase<Scalar> &X,
const Teuchos::Ptr<Thyra::MultiVectorBase<Scalar> > &Y,
const Scalar alpha,
const Scalar beta) const
{
using Teuchos::RCP;
using Teuchos::Ptr;
TEUCHOS_TEST_FOR_EXCEPTION(
!this->opSupported(M_trans),
Thyra::Exceptions::OpNotSupported,
this->description() << " does not support operation " << Thyra::toString(M_trans));
TEUCHOS_TEST_FOR_EXCEPTION(
!X.range()->isCompatible(*this->domain()),
Thyra::Exceptions::IncompatibleVectorSpaces,
"Domain of " << this->description() << ": " << this->domain()->description() <<
" is not compatible with column space of " << X.description() << ": " << X.range()->description());
TEUCHOS_TEST_FOR_EXCEPTION(
!Y->range()->isCompatible(*this->range()),
Thyra::Exceptions::IncompatibleVectorSpaces,
"Range of " << this->description() << ": " << this->range()->description() <<
" is not compatible with column space of " << Y->description() << ": " << Y->range()->description());
TEUCHOS_TEST_FOR_EXCEPTION(
!Y->domain()->isCompatible(*X.domain()),
Thyra::Exceptions::IncompatibleVectorSpaces,
"Row space of " << Y->description() << ": " << Y->domain()->description() <<
" is not compatible with row space of " << X.description() << ": " << X.domain()->description());
TEUCHOS_TEST_FOR_EXCEPTION(
&X == Y.get(),
std::logic_error,
"X and Y arguments are both aliases of " << X.description());
if (alpha == Teuchos::ScalarTraits<Scalar>::zero()) {
// Y <- beta * Y
Thyra::Vt_S(Y, beta);
return;
}
typedef typename Teuchos::ScalarTraits<Scalar>::magnitudeType ScalarMagnitude;
RCP<const Thyra::VectorBase<Scalar> > x_dot_base;
if (basePoint_.supports(Thyra::ModelEvaluatorBase::IN_ARG_x_dot))
x_dot_base = basePoint_.get_x_dot();
RCP<const Thyra::VectorBase<Scalar> > x_base = basePoint_.get_x();
if (Teuchos::is_null(x_base)) {
x_base = model_->getNominalValues().get_x();
}
x_base.assert_not_null();
const ScalarMagnitude norm_x_base = Thyra::norm_2(*x_base);
// Number of columns common to both vectors X and Y
// (X and Y have compatible row spaces)
const Thyra::Ordinal colCount = X.domain()->dim();
for (Teuchos::Ordinal j = Teuchos::Ordinal(); j < colCount; ++j) {
const RCP<const Thyra::VectorBase<Scalar> > X_vec = X.col(j);
const RCP<Thyra::VectorBase<Scalar> > Y_vec = Y->col(j);
const ScalarMagnitude norm_dx = Thyra::norm_2(*X_vec);
if (norm_dx == Teuchos::ScalarTraits<ScalarMagnitude>::zero()) {
if (beta == Teuchos::ScalarTraits<Scalar>::zero()) {
// Y_vec <- 0
Thyra::put_scalar(Teuchos::ScalarTraits<ScalarMagnitude>::zero(), Y_vec.ptr());
} else {
// Y_vec <- beta * Y_vec
Thyra::scale(beta, Y_vec.ptr());
}
} else {
// Scalar perturbation
const ScalarMagnitude relative_pert_ratio = static_cast<ScalarMagnitude>(lambda_);
const ScalarMagnitude eta = (relative_pert_ratio * ((norm_x_base / norm_dx) + relative_pert_ratio));
// Compute perturbed residual
// Dynamic: f_pert <- f(x_dot_base + eta * (W_alpha * X), x_base + eta * (W_beta * X))
// Static: f_pert <- f(x_base + eta * X)
const RCP<Thyra::VectorBase<Scalar> > f_pert = Thyra::createMember(this->range());
{
Thyra::ModelEvaluatorBase::InArgs<Scalar> pertInArgs = model_->createInArgs();
{
pertInArgs.setArgs(basePoint_);
const bool isDynamic = Teuchos::nonnull(x_dot_base);
if (isDynamic) {
const RCP<Thyra::VectorBase<Scalar> > x_dot_pert = Thyra::createMember(this->domain());
const Scalar W_alpha = pertInArgs.get_alpha();
Thyra::V_VpStV<Scalar>(x_dot_pert.ptr(), *x_dot_base, W_alpha * eta, *X_vec);
pertInArgs.set_x_dot(x_dot_pert);
}
const RCP<Thyra::VectorBase<Scalar> > x_pert = Thyra::createMember(this->domain());
const Scalar W_beta = isDynamic ? pertInArgs.get_beta() : Teuchos::ScalarTraits<Scalar>::one();
Thyra::V_VpStV<Scalar>(x_pert.ptr(), *x_base, W_beta * eta, *X_vec);
pertInArgs.set_x(x_pert);
}
Thyra::ModelEvaluatorBase::OutArgs<Scalar> pertOutArgs = model_->createOutArgs();
{
pertOutArgs.set_f(f_pert);
}
model_->evalModel(pertInArgs, pertOutArgs);
}
// Y <- alpha * (1/eta) * (f_pert - f_base) + beta * Y
const Scalar alpha_over_eta = alpha / eta;
if (beta == Teuchos::ScalarTraits<Scalar>::zero()) {
// Y <- alpha * (1/eta) * (f_pert - f_base)
Thyra::V_StVpStV<Scalar>(Y_vec.ptr(), alpha_over_eta, *f_pert, -alpha_over_eta, *f_base_);
} else {
// Aliasing f_pert and alpha_op_X (f_pert == alpha_op_X)
const RCP<Thyra::VectorBase<Scalar> > alpha_op_X = f_pert;
// alpha_op_X <- alpha * (1/eta) * (f_pert - f_base)
Thyra::Vp_StV(alpha_op_X.ptr(), -Teuchos::ScalarTraits<Scalar>::one(), *f_base_);
const Scalar alpha_over_eta = alpha / eta;
Thyra::Vt_S(alpha_op_X.ptr(), alpha_over_eta);
// Y <- alpha_op_X + beta * Y
Thyra::Vp_V<Scalar>(Y_vec.ptr(), *alpha_op_X, beta);
}
}
}
}