int get_entity_subcell_id(const BulkData& mesh,
const Entity entity,
const EntityRank subcell_rank,
stk::topology subcell_topology,
const std::vector<Entity>& subcell_nodes)
{
ThrowAssert(subcell_rank <= stk::topology::ELEMENT_RANK);
const int INVALID_SIDE = -1;
stk::topology entity_topology = mesh.bucket(entity).topology();
ThrowAssert(entity_topology.num_nodes() == mesh.num_nodes(entity));
const Entity* entity_nodes = mesh.begin_nodes(entity);
std::vector<Entity> topology_sub_nodes(subcell_nodes.size());
for(size_t i = 0; i < entity_topology.num_sub_topology(subcell_rank); ++i)
{
entity_topology.sub_topology_nodes(entity_nodes, subcell_rank, i, topology_sub_nodes.begin());
if(subcell_topology.equivalent(topology_sub_nodes, subcell_nodes).first)
{
return i;
}
}
return INVALID_SIDE;
}
inline
typename FieldTraits<FieldType>::data_type*
field_data(const FieldType & f, const Bucket& b, Bucket::size_type bucket_ord) {
ThrowAssert(f.entity_rank() == b.entity_rank());
ThrowAssert(&f.get_mesh() == &b.mesh());
const FieldMetaData& field_meta_data = f.get_meta_data_for_field()[b.bucket_id()];
return reinterpret_cast<typename FieldTraits<FieldType>::data_type*>(field_meta_data.m_data + field_meta_data.m_bytes_per_entity * bucket_ord);
}
inline
typename FieldTraits<FieldType>::data_type*
field_data(const FieldType & f, Entity e)
{
const MeshIndex& mi = f.get_mesh().mesh_index(e);
ThrowAssert(f.entity_rank() == mi.bucket->entity_rank());
ThrowAssert(&f.get_mesh() == &mi.bucket->mesh());
const FieldMetaData& field_meta_data = f.get_meta_data_for_field()[mi.bucket->bucket_id()];
return reinterpret_cast<typename FieldTraits<FieldType>::data_type*>(field_meta_data.m_data + field_meta_data.m_bytes_per_entity * mi.bucket_ordinal);
}
bool Entity::update_relation(
const RelationIterator ir ,
const bool back_rel_flag) const
{
const Relation::RelationType relType = ir->getRelationType();
ThrowAssert(verify_relation_ordering(internal_begin_relation(relType), internal_end_relation(relType)));
ThrowAssertMsg(!internal_is_handled_generically(relType),
"update_relation should not be called for STK-managed relations");
Entity & meshObj = *ir->getMeshObj() ;
const Relation::RelationType backRelType = back_relation_type(relType);
ThrowAssert(verify_relation_ordering(meshObj.internal_begin_relation(backRelType), meshObj.internal_end_relation(backRelType)));
// Create the corresponding back relation to ir
Relation backRel_obj(const_cast<Entity*>(this), backRelType, ir->getOrdinal(), ir->getOrientation());
RelationIterator backRel_itr = meshObj.find_relation(backRel_obj);
const bool exists = backRel_itr != meshObj.internal_end_relation(backRelType) && *backRel_itr == backRel_obj;
if (exists && !back_rel_flag) {
// Remove back relation and increment the counter
meshObj.erase_and_clear_if_empty(backRel_itr);
//ThrowAssert(sierra::Fmwk::get_derived_type(meshObj) != Entity::ELEMENT);
meshObj.inc_connection();
}
else if (!exists && back_rel_flag) {
// Insert back relation
const unsigned k = backRel_itr - meshObj.internal_begin_relation(backRelType) ;
meshObj.reserve_relation(meshObj.aux_relations().size() + 1);
meshObj.aux_relations().insert(meshObj.aux_relations().begin() + k, backRel_obj);
//ThrowAssert(sierra::Fmwk::get_derived_type(meshObj) != Entity::ELEMENT);
meshObj.dec_connection();
}
ThrowAssert(verify_relation_ordering(meshObj.internal_begin_relation(relType), meshObj.internal_end_relation(relType)));
return true;
}
void
TemperaturePropAlgorithm::execute()
{
// make sure that partVec_ is size one
ThrowAssert( partVec_.size() == 1 );
std::vector<double> indVarList(1);
stk::mesh::Selector selector = stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& node_buckets =
realm_.get_buckets( stk::topology::NODE_RANK, selector );
for ( stk::mesh::BucketVector::const_iterator ib = node_buckets.begin();
ib != node_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
const stk::mesh::Bucket::size_type length = b.size();
double *prop = (double*) stk::mesh::field_data(*prop_, b);
const double *temperature = (double*) stk::mesh::field_data(*temperature_, b);
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
indVarList[0] = temperature[k];
prop[k] = propEvaluator_->execute(&indVarList[0], b[k]);
}
}
}
void
InverseDualVolumePropAlgorithm::execute()
{
// make sure that partVec_ is size one
ThrowAssert( partVec_.size() == 1 );
stk::mesh::Selector selector = stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& node_buckets =
realm_.get_buckets( stk::topology::NODE_RANK, selector );
for ( stk::mesh::BucketVector::const_iterator ib = node_buckets.begin();
ib != node_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
const stk::mesh::Bucket::size_type length = b.size();
double *prop = (double*)stk::mesh::field_data(*prop_, b);
const double *dualNodalVolume = (double*)stk::mesh::field_data(*dualNodalVolume_, b);
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
prop[k] = 1.0/dualNodalVolume[k];
}
}
}
inline
typename FieldTraits<FieldType>::data_type*
field_data(const FieldType & f, const unsigned bucket_id, Bucket::size_type bucket_ord, const int knownSize) {
ThrowAssertMsg(f.get_meta_data_for_field()[bucket_id].m_bytes_per_entity >= knownSize, "field name= " << f.name() << "knownSize= " << knownSize << ", m_bytes_per_entity= " << f.get_meta_data_for_field()[bucket_id].m_bytes_per_entity);
ThrowAssert(f.get_meta_data_for_field()[bucket_id].m_data != NULL);
return reinterpret_cast<typename FieldTraits<FieldType>::data_type*>(f.get_meta_data_for_field()[bucket_id].m_data + knownSize * bucket_ord);
}
MEField<> *FieldReg::GetCoordField() const {
Trace __trace("FieldReg::GetCoordField()");
MEField<> *cf = GetField("coordinates");
ThrowAssert(cf);
return cf;
}
void
LinearPropAlgorithm::execute()
{
// make sure that partVec_ is size one
ThrowAssert( partVec_.size() == 1 );
stk::mesh::Selector selector = stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& node_buckets =
realm_.get_buckets( stk::topology::NODE_RANK, selector );
for ( stk::mesh::BucketVector::const_iterator ib = node_buckets.begin();
ib != node_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
const stk::mesh::Bucket::size_type length = b.size();
double *prop = (double*) stk::mesh::field_data(*prop_, b);
const double *indVar = (double*) stk::mesh::field_data(*indVar_, b);
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
const double z = indVar[k];
const double om_z = 1.0-z;
prop[k] = z*primary_ + om_z*secondary_;
}
}
}
void internal_check_no_null_buckets_invariant() const
{
#ifndef NDEBUG
for (int i = 0, e = m_buckets.size(); i < e; ++i) {
ThrowAssert(m_buckets[i] != NULL);
}
#endif
}
BBox BBoxIntersection(const BBox &b1, const BBox &b2) {
BBox newbox(b1.dimension());
ThrowAssert(b1.dimension() == b2.dimension());
for (UInt i = 0; i < b1.dimension(); i++) {
newbox.setMin(i, std::max(b1.getMin()[i], b2.getMin()[i]));
newbox.setMax(i, std::min(b1.getMax()[i], b2.getMax()[i]));
}
newbox.checkEmpty();
return newbox;
}
void mat_chunk(
const Scalar* mat,
int nrows,
Scalar* chunk,
int istart,
int jstart,
int iend,
int jend)
{
// copies matrix section of column major square matrix into contiguous, row-major submatrix
ThrowAssert(istart >= 0 && istart < iend);
ThrowAssert(jstart >= 0 && jstart < jend);
ThrowAssert(iend <= nrows);
ThrowAssert(jend <= nrows);
int jj = 0;
for (int j = jstart; j < jend; ++j) {
for (int i = istart; i < iend; ++i, ++jj) {
chunk[jj] = mat[i*nrows + j];
}
}
}
stk::topology get_subcell_nodes(const BulkData& mesh, const Entity entity,
EntityRank subcell_rank,
unsigned subcell_identifier,
EntityVector & subcell_nodes)
{
ThrowAssert(subcell_rank <= stk::topology::ELEMENT_RANK);
subcell_nodes.clear();
// get cell topology
stk::topology celltopology = mesh.bucket(entity).topology();
//error checking
{
//no celltopology defined
if(celltopology == stk::topology::INVALID_TOPOLOGY)
{
return celltopology;
}
// valid ranks fall within the dimension of the cell topology
const bool bad_rank = subcell_rank >= celltopology.dimension();
ThrowInvalidArgMsgIf( bad_rank, "subcell_rank is >= celltopology dimension\n");
// subcell_identifier must be less than the subcell count
const bool bad_id = subcell_identifier >= celltopology.num_sub_topology(subcell_rank);
ThrowInvalidArgMsgIf( bad_id, "subcell_id is >= subcell_count\n");
}
// Get the cell topology of the subcell
stk::topology subcell_topology =
celltopology.sub_topology(subcell_rank, subcell_identifier);
const int num_nodes_in_subcell = subcell_topology.num_nodes();
// For the subcell, get it's local nodes ids
std::vector<unsigned> subcell_node_local_ids(num_nodes_in_subcell);
celltopology.sub_topology_node_ordinals(subcell_rank, subcell_identifier, subcell_node_local_ids.begin());
Entity const *node_relations = mesh.begin_nodes(entity);
subcell_nodes.reserve(num_nodes_in_subcell);
for(int i = 0; i < num_nodes_in_subcell; ++i)
{
subcell_nodes.push_back(node_relations[subcell_node_local_ids[i]]);
}
return subcell_topology;
}
bool BBoxIntersect(const BBox &b1, const BBox &b2, double tol) {
double newmin;
double newmax;
ThrowAssert(b1.dimension() == b2.dimension());
for (UInt i = 0; i < b1.dimension(); i++) {
newmin = std::max(b1.getMin()[i], b2.getMin()[i]);
newmax = std::min(b1.getMax()[i], b2.getMax()[i]);
if (newmin > (newmax+tol)) {
//std::cout << "fail, dim=" << i << " newmin=" << newmin << ", newmax=" << newmax << std::endl;
return false;
}
}
return true;
}
inline
void field_fill(
const Scalar data,
NgpFieldVector<Scalar> & xField,
const stk::mesh::Selector selector,
const MPI_Comm comm)
{
ThrowAssert(typeid(Scalar) == xField.get_field().data_traits().type_info);
stk::mesh::BucketVector const& buckets = xField.get_buckets(selector);
for(size_t i=0; i < buckets.size(); i++) {
stk::mesh::Bucket & b = *buckets[i];
KokkosBLAS<Scalar>::fill(field_length(xField, b), data, field_ptr(xField, b));
}
}
void MEField<_FIELD>::Addfield(_FIELD *f, UInt nval) {
// Store as a hash of fields by nval;
std::vector<UInt>::iterator i =
std::lower_bound(fidx_table.begin(), fidx_table.end(), nval);
// Error if already there
if (i == fidx_table.end() || *i != nval) {
i = fidx_table.insert(i, nval);
} else Throw() << "Field:" << fname << ", already added nval:" << nval;
// Insert field at same spot.
UInt pos = std::distance(fidx_table.begin(), i);
typename std::vector<_FIELD*>::iterator fi = fields.begin() + pos;
UInt cursize = fields.size();
if (cursize == 0) primaryfield = f;
// if nval is larger, resize. Keeps old fields, assigns null elsewhere
ThrowAssert(fields.size() <= pos);
fields.insert(fi, f);
}
//--------------------------------------------------------------------------
void ElementCondenser::compute_interior_update(
double* lhs, const double* rhs,
const double* boundary_values, double* delta_interior_values)
{
// Computes an update to the interior values given the updated rhs vector
// and the elemental linear system
mat_chunk(lhs, ne_,
lhsII_.data(),
nb_, nb_,
ne_, ne_
);
int jj = 0;
for (int j = nb_; j < ne_; ++j, ++jj) {
delta_interior_values[jj] = rhs[j];
}
// solve for update L_II^-1 rhs_I
int info = 0;
lapack_.GESV(ni_, 1, lhsII_.data(), ni_, ipiv_.data(), delta_interior_values, ni_, &info);
ThrowAssert(info == 0);
}
Entity declare_element(BulkData & mesh,
PartVector & parts,
const EntityId elem_id,
const EntityIdVector & node_ids)
{
MetaData & fem_meta = MetaData::get(mesh);
stk::topology top = fem_meta.get_topology(*parts[0]);
ThrowAssert(node_ids.size() >= top.num_nodes());
ThrowErrorMsgIf(top == stk::topology::INVALID_TOPOLOGY,
"Part " << parts[0]->name() << " does not have a local topology");
PartVector empty;
const EntityRank entity_rank = stk::topology::ELEMENT_RANK;
Entity elem = mesh.declare_entity(entity_rank, elem_id, parts);
const EntityRank node_rank = stk::topology::NODE_RANK;
Permutation perm = stk::mesh::Permutation::INVALID_PERMUTATION;
OrdinalVector ordinal_scratch;
ordinal_scratch.reserve(64);
PartVector part_scratch;
part_scratch.reserve(64);
for(unsigned i = 0; i < top.num_nodes(); ++i)
{
//declare node if it doesn't already exist
Entity node = mesh.get_entity(node_rank, node_ids[i]);
if(!mesh.is_valid(node))
{
node = mesh.declare_entity(node_rank, node_ids[i], empty);
}
mesh.declare_relation(elem, node, i, perm, ordinal_scratch, part_scratch);
}
return elem;
}
inline
void field_asum(
Scalar & glob_result,
NgpFieldVector<Scalar>& xField,
const stk::mesh::Selector& selector,
const MPI_Comm comm)
{
ThrowAssert(typeid(Scalar) == xField.get_field().data_traits().type_info);
stk::mesh::BucketVector const& buckets = xField.get_buckets(selector);
KokkosVector& dev_x = xField.device_get();
Scalar local_result = Scalar(0.0);
for(size_t i=0; i < buckets.size(); i++) {
stk::mesh::Bucket & b = *buckets[i];
int kmax = field_length(xField, b);
xField.copy_to_device(kmax, field_ptr(xField, b));
Scalar gpu_result = Scalar(0.0);
Kokkos::parallel_reduce( range_policy( 0, kmax), KOKKOS_LAMBDA ( int k, double& update ) {
update += dev_x( k );
}, gpu_result );
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleMeshDisplacementElemSolverAlgorithm::execute()
{
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
// space for LHS/RHS; nodesPerElem*nDim*nodesPerElem*nDim and nodesPerElem*nDim
std::vector<double> lhs;
std::vector<double> rhs;
std::vector<int> scratchIds;
std::vector<double> scratchVals;
std::vector<stk::mesh::Entity> connected_nodes;
// nodal fields to gather
std::vector<double> ws_displacementNp1;
std::vector<double> ws_coordinates;
std::vector<double> ws_modelCoordinates;
std::vector<double> ws_mu;
std::vector<double> ws_lambda;
// geometry related to populate
std::vector<double> ws_scs_areav;
std::vector<double> ws_dndx;
std::vector<double> ws_deriv;
std::vector<double> ws_det_j;
std::vector<double> ws_shape_function;
// deal with state
VectorFieldType &displacementNp1 = meshDisplacement_->field_of_state(stk::mesh::StateNP1);
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
&stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& elem_buckets =
realm_.get_buckets( stk::topology::ELEMENT_RANK, s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = elem_buckets.begin();
ib != elem_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
const stk::mesh::Bucket::size_type length = b.size();
// extract master element
MasterElement *meSCS = sierra::nalu::MasterElementRepo::get_surface_master_element(b.topology());
// extract master element specifics
const int nodesPerElement = meSCS->nodesPerElement_;
const int numScsIp = meSCS->numIntPoints_;
const int *lrscv = meSCS->adjacentNodes();
// resize some things; matrix related
const int lhsSize = nodesPerElement*nDim*nodesPerElement*nDim;
const int rhsSize = nodesPerElement*nDim;
lhs.resize(lhsSize);
rhs.resize(rhsSize);
scratchIds.resize(rhsSize);
scratchVals.resize(rhsSize);
connected_nodes.resize(nodesPerElement);
// algorithm related
ws_displacementNp1.resize(nodesPerElement*nDim);
ws_coordinates.resize(nodesPerElement*nDim);
ws_modelCoordinates.resize(nodesPerElement*nDim);
ws_mu.resize(nodesPerElement);
ws_lambda.resize(nodesPerElement);
ws_scs_areav.resize(numScsIp*nDim);
ws_dndx.resize(nDim*numScsIp*nodesPerElement);
ws_deriv.resize(nDim*numScsIp*nodesPerElement);
ws_det_j.resize(numScsIp);
ws_shape_function.resize(numScsIp*nodesPerElement);
// pointer to lhs/rhs
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
double *p_displacementNp1 = &ws_displacementNp1[0];
double *p_coordinates = &ws_coordinates[0];
double *p_modelCoordinates = &ws_modelCoordinates[0];
double *p_mu = &ws_mu[0];
double *p_lambda = &ws_lambda[0];
double *p_scs_areav = &ws_scs_areav[0];
double *p_dndx = &ws_dndx[0];
double *p_shape_function = &ws_shape_function[0];
// extract shape function
meSCS->shape_fcn(&p_shape_function[0]);
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// zero lhs/rhs
for ( int p = 0; p < lhsSize; ++p )
p_lhs[p] = 0.0;
for ( int p = 0; p < rhsSize; ++p )
p_rhs[p] = 0.0;
//===============================================
// gather nodal data; this is how we do it now..
//===============================================
stk::mesh::Entity const * node_rels = b.begin_nodes(k);
int num_nodes = b.num_nodes(k);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
stk::mesh::Entity node = node_rels[ni];
// set connected nodes
connected_nodes[ni] = node;
// pointers to real data
const double * dxNp1 = stk::mesh::field_data(displacementNp1, node);
const double * coords = stk::mesh::field_data(*coordinates_, node);
const double * modelCoords = stk::mesh::field_data(*modelCoordinates_, node);
const double mu = *stk::mesh::field_data(*mu_, node);
const double lambda = *stk::mesh::field_data(*lambda_, node);
// gather scalars
p_mu[ni] = mu;
p_lambda[ni] = lambda;
// gather vectors
const int niNdim = ni*nDim;
for ( int i=0; i < nDim; ++i ) {
p_displacementNp1[niNdim+i] = dxNp1[i];
p_coordinates[niNdim+i] = coords[i];
p_modelCoordinates[niNdim+i] = modelCoords[i];
}
}
// compute geometry
double scs_error = 0.0;
meSCS->determinant(1, &p_coordinates[0], &p_scs_areav[0], &scs_error);
// compute dndx; model coords or displaced?
if ( deformWrtModelCoords_ ) {
meSCS->grad_op(1, &p_modelCoordinates[0], &p_dndx[0], &ws_deriv[0], &ws_det_j[0], &scs_error);
}
else {
meSCS->grad_op(1, &p_coordinates[0], &p_dndx[0], &ws_deriv[0], &ws_det_j[0], &scs_error);
}
for ( int ip = 0; ip < numScsIp; ++ip ) {
const int ipNdim = ip*nDim;
const int offSetSF = ip*nodesPerElement;
// left and right nodes for this ip
const int il = lrscv[2*ip];
const int ir = lrscv[2*ip+1];
// save off some offsets
const int ilNdim = il*nDim;
const int irNdim = ir*nDim;
// compute scs point values; offset to Shape Function; sneak in divU
double muIp = 0.0;
double lambdaIp = 0.0;
double divDx = 0.0;
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
const double r = p_shape_function[offSetSF+ic];
muIp += r*p_mu[ic];
lambdaIp += r*p_lambda[ic];
const int offSetDnDx = nDim*nodesPerElement*ip + ic*nDim;
for ( int j = 0; j < nDim; ++j ) {
const double dxj = p_displacementNp1[ic*nDim+j];
divDx += dxj*p_dndx[offSetDnDx+j];
}
}
// assemble divDx term (explicit)
for ( int i = 0; i < nDim; ++i ) {
// divU stress term
const double divTerm = -lambdaIp*divDx*p_scs_areav[ipNdim+i];
const int indexL = ilNdim + i;
const int indexR = irNdim + i;
// right hand side; L and R
p_rhs[indexL] -= divTerm;
p_rhs[indexR] += divTerm;
}
// stress
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
const int icNdim = ic*nDim;
for ( int i = 0; i < nDim; ++i ) {
const int indexL = ilNdim + i;
const int indexR = irNdim + i;
const int rowL = indexL*nodesPerElement*nDim;
const int rowR = indexR*nodesPerElement*nDim;
const int rLiC_i = rowL+icNdim+i;
const int rRiC_i = rowR+icNdim+i;
// viscous stress
const int offSetDnDx = nDim*nodesPerElement*ip + icNdim;
double lhs_riC_i = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double axj = p_scs_areav[ipNdim+j];
const double dxj = p_displacementNp1[icNdim+j];
// -mu*dxi/dxj*A_j; fixed i over j loop; see below..
const double lhsfacDiff_i = -muIp*p_dndx[offSetDnDx+j]*axj;
// lhs; il then ir
lhs_riC_i += lhsfacDiff_i;
// -mu*dxj/dxi*A_j
const double lhsfacDiff_j = -muIp*p_dndx[offSetDnDx+i]*axj;
// lhs; il then ir
p_lhs[rowL+icNdim+j] += lhsfacDiff_j;
p_lhs[rowR+icNdim+j] -= lhsfacDiff_j;
// rhs; il then ir
p_rhs[indexL] -= lhsfacDiff_j*dxj;
p_rhs[indexR] += lhsfacDiff_j*dxj;
}
// deal with accumulated lhs and flux for -mu*dxi/dxj*Aj
p_lhs[rLiC_i] += lhs_riC_i;
p_lhs[rRiC_i] -= lhs_riC_i;
const double dxi = p_displacementNp1[icNdim+i];
p_rhs[indexL] -= lhs_riC_i*dxi;
p_rhs[indexR] += lhs_riC_i*dxi;
}
}
}
apply_coeff(connected_nodes, scratchIds, scratchVals, rhs, lhs, __FILE__);
}
}
}
//--------------------------------------------------------------------------
//-------- elem_execute ----------------------------------------------------
//--------------------------------------------------------------------------
void
MomentumMassBackwardEulerElemSuppAlg::elem_execute(
double *lhs,
double *rhs,
stk::mesh::Entity element,
MasterElement */*meSCS*/,
MasterElement *meSCV)
{
// pointer to ME methods
const int *ipNodeMap = meSCV->ipNodeMap();
const int nodesPerElement = meSCV->nodesPerElement_;
const int numScvIp = meSCV->numIntPoints_;
// gather
stk::mesh::Entity const * node_rels = bulkData_->begin_nodes(element);
int num_nodes = bulkData_->num_nodes(element);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
stk::mesh::Entity node = node_rels[ni];
// pointers to real data
const double * uN = stk::mesh::field_data(*velocityN_, node );
const double * uNp1 = stk::mesh::field_data(*velocityNp1_, node );
const double * Gjp = stk::mesh::field_data(*Gjp_, node );
const double * coords = stk::mesh::field_data(*coordinates_, node);
// gather scalars
ws_rhoN_[ni] = *stk::mesh::field_data(*densityN_, node);
ws_rhoNp1_[ni] = *stk::mesh::field_data(*densityNp1_, node);
// gather vectors
const int niNdim = ni*nDim_;
for ( int j=0; j < nDim_; ++j ) {
ws_uN_[niNdim+j] = uN[j];
ws_uNp1_[niNdim+j] = uNp1[j];
ws_Gjp_[niNdim+j] = Gjp[j];
ws_coordinates_[niNdim+j] = coords[j];
}
}
// compute geometry
double scv_error = 0.0;
meSCV->determinant(1, &ws_coordinates_[0], &ws_scv_volume_[0], &scv_error);
for ( int ip = 0; ip < numScvIp; ++ip ) {
// nearest node to ip
const int nearestNode = ipNodeMap[ip];
// zero out; scalar and vector
double rhoNScv = 0.0;
double rhoNp1Scv = 0.0;
for ( int j =0; j < nDim_; ++j ) {
uNScv_[j] = 0.0;
uNp1Scv_[j] = 0.0;
GjpScv_[j] = 0.0;
}
const int offSet = ip*nodesPerElement;
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
// save off shape function
const double r = ws_shape_function_[offSet+ic];
// density
rhoNScv += r*ws_rhoN_[ic];
rhoNp1Scv += r*ws_rhoNp1_[ic];
// velocity
const int icNdim = ic*nDim_;
for ( int j = 0; j < nDim_; ++j ) {
uNScv_[j] += r*ws_uN_[icNdim+j];
uNp1Scv_[j] += r*ws_uNp1_[icNdim+j];
GjpScv_[j] += r*ws_Gjp_[icNdim+j];
}
}
// assemble rhs
const double scV = ws_scv_volume_[ip];
const int nnNdim = nearestNode*nDim_;
for ( int i = 0; i < nDim_; ++i ) {
rhs[nnNdim+i] +=
-(rhoNp1Scv*uNp1Scv_[i]-rhoNScv*uNScv_[i])*scV/dt_
-GjpScv_[i]*scV; //- ws_Gjp_[nnNdim+i]*scV;
}
// manage LHS
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
const int icNdim = ic*nDim_;
// save off shape function
const double r = ws_shape_function_[offSet+ic];
const double lhsfac = r*rhoNp1Scv*scV/dt_;
for ( int i = 0; i < nDim_; ++i ) {
const int indexNN = nnNdim + i;
const int rowNN = indexNN*nodesPerElement*nDim_;
const int rNNiC_i = rowNN+icNdim+i;
lhs[rNNiC_i] += lhsfac;
}
}
}
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleMomentumEdgeSolverAlgorithm::execute()
{
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
const double small = 1.0e-16;
// extract user advection options (allow to potentially change over time)
const std::string dofName = "velocity";
const double alpha = realm_.get_alpha_factor(dofName);
const double alphaUpw = realm_.get_alpha_upw_factor(dofName);
const double hoUpwind = realm_.get_upw_factor(dofName);
const bool useLimiter = realm_.primitive_uses_limiter(dofName);
// one minus flavor
const double om_alpha = 1.0-alpha;
const double om_alphaUpw = 1.0-alphaUpw;
// space for LHS/RHS; always edge connectivity
const int nodesPerEdge = 2;
const int lhsSize = nDim*nodesPerEdge*nDim*nodesPerEdge;
const int rhsSize = nDim*nodesPerEdge;
std::vector<double> lhs(lhsSize);
std::vector<double> rhs(rhsSize);
std::vector<stk::mesh::Entity> connected_nodes(2);
// area vector; gather into
std::vector<double> areaVec(nDim);
// pointer for fast access
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
double *p_areaVec = &areaVec[0];
// space for dui/dxj. This variable is the modified gradient with NOC
std::vector<double> duidxj(nDim*nDim);
// extrapolated value from the L/R direction
std::vector<double> uIpL(nDim);
std::vector<double> uIpR(nDim);
// limiter values from the L/R direction, 0:1
std::vector<double> limitL(nDim,1.0);
std::vector<double> limitR(nDim,1.0);
// extrapolated gradient from L/R direction
std::vector<double> duL(nDim);
std::vector<double> duR(nDim);
// pointers for fast access
double *p_duidxj = &duidxj[0];
double *p_uIpL = &uIpL[0];
double *p_uIpR = &uIpR[0];
double *p_limitL = &limitL[0];
double *p_limitR = &limitR[0];
double *p_duL = &duL[0];
double *p_duR = &duR[0];
// deal with state
VectorFieldType &velocityNp1 = velocity_->field_of_state(stk::mesh::StateNP1);
ScalarFieldType &densityNp1 = density_->field_of_state(stk::mesh::StateNP1);
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
& stk::mesh::selectUnion(partVec_)
& !(realm_.get_inactive_selector());
stk::mesh::BucketVector const& edge_buckets =
realm_.get_buckets( stk::topology::EDGE_RANK, s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = edge_buckets.begin();
ib != edge_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
const stk::mesh::Bucket::size_type length = b.size();
// pointer to edge area vector and mdot
const double * av = stk::mesh::field_data(*edgeAreaVec_, b);
const double * mdot = stk::mesh::field_data(*massFlowRate_, b);
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// zeroing of lhs/rhs
for ( int i = 0; i < lhsSize; ++i ) {
p_lhs[i] = 0.0;
}
for ( int i = 0; i < rhsSize; ++i ) {
p_rhs[i] = 0.0;
}
stk::mesh::Entity const * edge_node_rels = b.begin_nodes(k);
// pointer to edge area vector
for ( int j = 0; j < nDim; ++j )
p_areaVec[j] = av[k*nDim+j];
const double tmdot = mdot[k];
// sanity check on number or nodes
ThrowAssert( b.num_nodes(k) == 2 );
// left and right nodes
stk::mesh::Entity nodeL = edge_node_rels[0];
stk::mesh::Entity nodeR = edge_node_rels[1];
connected_nodes[0] = nodeL;
connected_nodes[1] = nodeR;
// extract nodal fields
const double * coordL = stk::mesh::field_data(*coordinates_, nodeL);
const double * coordR = stk::mesh::field_data(*coordinates_, nodeR);
const double * dudxL = stk::mesh::field_data(*dudx_, nodeL);
const double * dudxR = stk::mesh::field_data(*dudx_, nodeR);
const double * vrtmL = stk::mesh::field_data(*velocityRTM_, nodeL);
const double * vrtmR = stk::mesh::field_data(*velocityRTM_, nodeR);
const double * uNp1L = stk::mesh::field_data(velocityNp1, nodeL);
const double * uNp1R = stk::mesh::field_data(velocityNp1, nodeR);
const double densityL = *stk::mesh::field_data(densityNp1, nodeL);
const double densityR = *stk::mesh::field_data(densityNp1, nodeR);
const double viscosityL = *stk::mesh::field_data(*viscosity_, nodeL);
const double viscosityR = *stk::mesh::field_data(*viscosity_, nodeR);
// copy in extrapolated values
for ( int i = 0; i < nDim; ++i ) {
// extrapolated du
p_duL[i] = 0.0;
p_duR[i] = 0.0;
const int offSet = nDim*i;
for ( int j = 0; j < nDim; ++j ) {
const double dxj = 0.5*(coordR[j] - coordL[j]);
p_duL[i] += dxj*dudxL[offSet+j];
p_duR[i] += dxj*dudxR[offSet+j];
}
}
// compute geometry
double axdx = 0.0;
double asq = 0.0;
double udotx = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double axj = p_areaVec[j];
const double dxj = coordR[j] - coordL[j];
axdx += axj*dxj;
asq += axj*axj;
udotx += 0.5*dxj*(vrtmL[j] + vrtmR[j]);
}
const double inv_axdx = 1.0/axdx;
// ip props
const double viscIp = 0.5*(viscosityL + viscosityR);
const double diffIp = 0.5*(viscosityL/densityL + viscosityR/densityR);
// Peclet factor
const double pecfac = pecletFunction_->execute(std::abs(udotx)/(diffIp+small));
const double om_pecfac = 1.0-pecfac;
// determine limiter if applicable
if ( useLimiter ) {
for ( int i = 0; i < nDim; ++i ) {
const double dq = uNp1R[i] - uNp1L[i];
const double dqMl = 2.0*2.0*p_duL[i] - dq;
const double dqMr = 2.0*2.0*p_duR[i] - dq;
p_limitL[i] = van_leer(dqMl, dq, small);
p_limitR[i] = van_leer(dqMr, dq, small);
}
}
// final upwind extrapolation; with limiter
for ( int i = 0; i < nDim; ++i ) {
p_uIpL[i] = uNp1L[i] + p_duL[i]*hoUpwind*p_limitL[i];
p_uIpR[i] = uNp1R[i] - p_duR[i]*hoUpwind*p_limitR[i];
}
/*
form duidxj with over-relaxed procedure of Jasak:
dui/dxj = GjUi +[(uiR - uiL) - GlUi*dxl]*Aj/AxDx
where Gp is the interpolated pth nodal gradient for ui
*/
for ( int i = 0; i < nDim; ++i ) {
// difference between R and L nodes for component i
const double uidiff = uNp1R[i] - uNp1L[i];
// offset into all forms of dudx
const int offSetI = nDim*i;
// start sum for NOC contribution
double GlUidxl = 0.0;
for ( int l = 0; l< nDim; ++l ) {
const int offSetIL = offSetI+l;
const double dxl = coordR[l] - coordL[l];
const double GlUi = 0.5*(dudxL[offSetIL] + dudxR[offSetIL]);
GlUidxl += GlUi*dxl;
}
// form full tensor dui/dxj with NOC
for ( int j = 0; j < nDim; ++j ) {
const int offSetIJ = offSetI+j;
const double axj = p_areaVec[j];
const double GjUi = 0.5*(dudxL[offSetIJ] + dudxR[offSetIJ]);
p_duidxj[offSetIJ] = GjUi + (uidiff - GlUidxl)*axj*inv_axdx;
}
}
// lhs diffusion; only -mu*dui/dxj*Aj contribution for now
const double dlhsfac = -viscIp*asq*inv_axdx;
for ( int i = 0; i < nDim; ++i ) {
// 2nd order central
const double uiIp = 0.5*(uNp1R[i] + uNp1L[i]);
// upwind
const double uiUpwind = (tmdot > 0) ? alphaUpw*p_uIpL[i] + om_alphaUpw*uiIp
: alphaUpw*p_uIpR[i] + om_alphaUpw*uiIp;
// generalized central (2nd and 4th order)
const double uiHatL = alpha*p_uIpL[i] + om_alpha*uiIp;
const double uiHatR = alpha*p_uIpR[i] + om_alpha*uiIp;
const double uiCds = 0.5*(uiHatL + uiHatR);
// total advection; pressure contribution in time term expression
const double aflux = tmdot*(pecfac*uiUpwind + om_pecfac*uiCds);
// divU
double divU = 0.0;
for ( int j = 0; j < nDim; ++j)
divU += p_duidxj[j*nDim+j];
// diffusive flux; viscous tensor doted with area vector
double dflux = 2.0/3.0*viscIp*divU*p_areaVec[i]*includeDivU_;
const int offSetI = nDim*i;
for ( int j = 0; j < nDim; ++j ) {
const int offSetTrans = nDim*j+i;
const double axj = p_areaVec[j];
dflux += -viscIp*(p_duidxj[offSetI+j] + p_duidxj[offSetTrans])*axj;
}
// residal for total flux
const double tflux = aflux + dflux;
const int indexL = i;
const int indexR = i + nDim;
// total flux left
p_rhs[indexL] -= tflux;
// total flux right
p_rhs[indexR] += tflux;
// setup for LHS
const int rowL = indexL * nodesPerEdge*nDim;
const int rowR = indexR * nodesPerEdge*nDim;
//==============================
// advection first
//==============================
const int rLiL = rowL+indexL;
const int rLiR = rowL+indexR;
const int rRiL = rowR+indexL;
const int rRiR = rowR+indexR;
// upwind advection (includes 4th); left node
double alhsfac = 0.5*(tmdot+std::abs(tmdot))*pecfac*alphaUpw
+ 0.5*alpha*om_pecfac*tmdot;
p_lhs[rLiL] += alhsfac;
p_lhs[rRiL] -= alhsfac;
// upwind advection (incldues 4th); right node
alhsfac = 0.5*(tmdot-std::abs(tmdot))*pecfac*alphaUpw
+ 0.5*alpha*om_pecfac*tmdot;
p_lhs[rRiR] -= alhsfac;
p_lhs[rLiR] += alhsfac;
// central; left; collect terms on alpha and alphaUpw
alhsfac = 0.5*tmdot*(pecfac*om_alphaUpw + om_pecfac*om_alpha);
p_lhs[rLiL] += alhsfac;
p_lhs[rLiR] += alhsfac;
// central; right
p_lhs[rRiL] -= alhsfac;
p_lhs[rRiR] -= alhsfac;
//==============================
// diffusion second
//==============================
const double axi = p_areaVec[i];
//diffusion; row IL
p_lhs[rLiL] -= dlhsfac;
p_lhs[rLiR] += dlhsfac;
// diffusion; row IR
p_lhs[rRiL] += dlhsfac;
p_lhs[rRiR] -= dlhsfac;
// more diffusion; see theory manual
for ( int j = 0; j < nDim; ++j ) {
const double lhsfacNS = -viscIp*axi*p_areaVec[j]*inv_axdx;
const int colL = j;
const int colR = j + nDim;
// first left; IL,IL; IL,IR
p_lhs[rowL + colL] -= lhsfacNS;
p_lhs[rowL + colR] += lhsfacNS;
// now right, IR,IL; IR,IR
p_lhs[rowR + colL] += lhsfacNS;
p_lhs[rowR + colR] -= lhsfacNS;
}
}
apply_coeff(connected_nodes, rhs, lhs, __FILE__);
}
}
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleContinuityElemSolverAlgorithm::execute()
{
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
// time step
const double dt = realm_.get_time_step();
const double gamma1 = realm_.get_gamma1();
const double projTimeScale = dt/gamma1;
// deal with interpolation procedure
const double interpTogether = realm_.get_mdot_interp();
const double om_interpTogether = 1.0-interpTogether;
// space for LHS/RHS; nodesPerElem*nodesPerElem and nodesPerElem
std::vector<double> lhs;
std::vector<double> rhs;
std::vector<stk::mesh::Entity> connected_nodes;
// supplemental algorithm setup
const size_t supplementalAlgSize = supplementalAlg_.size();
for ( size_t i = 0; i < supplementalAlgSize; ++i )
supplementalAlg_[i]->setup();
// nodal fields to gather
std::vector<double> ws_vrtm;
std::vector<double> ws_Gpdx;
std::vector<double> ws_coordinates;
std::vector<double> ws_pressure;
std::vector<double> ws_density;
// geometry related to populate
std::vector<double> ws_scs_areav;
std::vector<double> ws_dndx;
std::vector<double> ws_dndx_lhs;
std::vector<double> ws_deriv;
std::vector<double> ws_det_j;
std::vector<double> ws_shape_function;
// integration point data that depends on size
std::vector<double> uIp(nDim);
std::vector<double> rho_uIp(nDim);
std::vector<double> GpdxIp(nDim);
std::vector<double> dpdxIp(nDim);
// pointers to everyone...
double *p_uIp = &uIp[0];
double *p_rho_uIp = &rho_uIp[0];
double *p_GpdxIp = &GpdxIp[0];
double *p_dpdxIp = &dpdxIp[0];
// deal with state
ScalarFieldType &densityNp1 = density_->field_of_state(stk::mesh::StateNP1);
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
& stk::mesh::selectUnion(partVec_)
& !(realm_.get_inactive_selector());
stk::mesh::BucketVector const& elem_buckets =
realm_.get_buckets( stk::topology::ELEMENT_RANK, s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = elem_buckets.begin();
ib != elem_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
const stk::mesh::Bucket::size_type length = b.size();
// extract master element
MasterElement *meSCS = realm_.get_surface_master_element(b.topology());
MasterElement *meSCV = realm_.get_volume_master_element(b.topology());
// extract master element specifics
const int nodesPerElement = meSCS->nodesPerElement_;
const int numScsIp = meSCS->numIntPoints_;
const int *lrscv = meSCS->adjacentNodes();
// resize some things; matrix related
const int lhsSize = nodesPerElement*nodesPerElement;
const int rhsSize = nodesPerElement;
lhs.resize(lhsSize);
rhs.resize(rhsSize);
connected_nodes.resize(nodesPerElement);
// algorithm related
ws_vrtm.resize(nodesPerElement*nDim);
ws_Gpdx.resize(nodesPerElement*nDim);
ws_coordinates.resize(nodesPerElement*nDim);
ws_pressure.resize(nodesPerElement);
ws_density.resize(nodesPerElement);
ws_scs_areav.resize(numScsIp*nDim);
ws_dndx.resize(nDim*numScsIp*nodesPerElement);
ws_dndx_lhs.resize(nDim*numScsIp*nodesPerElement);
ws_deriv.resize(nDim*numScsIp*nodesPerElement);
ws_det_j.resize(numScsIp);
ws_shape_function.resize(numScsIp*nodesPerElement);
// pointers
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
double *p_vrtm = &ws_vrtm[0];
double *p_Gpdx = &ws_Gpdx[0];
double *p_coordinates = &ws_coordinates[0];
double *p_pressure = &ws_pressure[0];
double *p_density = &ws_density[0];
double *p_scs_areav = &ws_scs_areav[0];
double *p_dndx = &ws_dndx[0];
double *p_dndx_lhs = reducedSensitivities_ ? &ws_dndx_lhs[0] : &ws_dndx[0];
double *p_shape_function = &ws_shape_function[0];
if ( shiftMdot_)
meSCS->shifted_shape_fcn(&p_shape_function[0]);
else
meSCS->shape_fcn(&p_shape_function[0]);
// resize possible supplemental element alg
for ( size_t i = 0; i < supplementalAlgSize; ++i )
supplementalAlg_[i]->elem_resize(meSCS, meSCV);
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// get elem
stk::mesh::Entity elem = b[k];
// zero lhs/rhs
for ( int p = 0; p < lhsSize; ++p )
p_lhs[p] = 0.0;
for ( int p = 0; p < rhsSize; ++p )
p_rhs[p] = 0.0;
//===============================================
// gather nodal data; this is how we do it now..
//===============================================
stk::mesh::Entity const * node_rels = b.begin_nodes(k);
int num_nodes = b.num_nodes(k);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
stk::mesh::Entity node = node_rels[ni];
// set connected nodes
connected_nodes[ni] = node;
// pointers to real data
const double * Gjp = stk::mesh::field_data(*Gpdx_, node );
const double * coords = stk::mesh::field_data(*coordinates_, node );
const double * vrtm = stk::mesh::field_data(*velocityRTM_, node );
// gather scalars
p_pressure[ni] = *stk::mesh::field_data(*pressure_, node );
p_density[ni] = *stk::mesh::field_data(densityNp1, node );
// gather vectors
const int niNdim = ni*nDim;
for ( int j=0; j < nDim; ++j ) {
p_vrtm[niNdim+j] = vrtm[j];
p_Gpdx[niNdim+j] = Gjp[j];
p_coordinates[niNdim+j] = coords[j];
}
}
// compute geometry
double scs_error = 0.0;
meSCS->determinant(1, &p_coordinates[0], &p_scs_areav[0], &scs_error);
// compute dndx for residual
if ( shiftPoisson_ )
meSCS->shifted_grad_op(1, &p_coordinates[0], &ws_dndx[0], &ws_deriv[0], &ws_det_j[0], &scs_error);
else
meSCS->grad_op(1, &p_coordinates[0], &ws_dndx[0], &ws_deriv[0], &ws_det_j[0], &scs_error);
// compute dndx for LHS
if ( reducedSensitivities_ )
meSCS->shifted_grad_op(1, &p_coordinates[0], &ws_dndx_lhs[0], &ws_deriv[0], &ws_det_j[0], &scs_error);
for ( int ip = 0; ip < numScsIp; ++ip ) {
// left and right nodes for this ip
const int il = lrscv[2*ip];
const int ir = lrscv[2*ip+1];
// corresponding matrix rows
int rowL = il*nodesPerElement;
int rowR = ir*nodesPerElement;
// setup for ip values; sneak in geometry for possible reduced sens
for ( int j = 0; j < nDim; ++j ) {
p_uIp[j] = 0.0;
p_rho_uIp[j] = 0.0;
p_GpdxIp[j] = 0.0;
p_dpdxIp[j] = 0.0;
}
double rhoIp = 0.0;
const int offSet = ip*nodesPerElement;
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
const double r = p_shape_function[offSet+ic];
const double nodalPressure = p_pressure[ic];
const double nodalRho = p_density[ic];
rhoIp += r*nodalRho;
double lhsfac = 0.0;
const int offSetDnDx = nDim*nodesPerElement*ip + ic*nDim;
for ( int j = 0; j < nDim; ++j ) {
p_GpdxIp[j] += r*p_Gpdx[nDim*ic+j];
p_uIp[j] += r*p_vrtm[nDim*ic+j];
p_rho_uIp[j] += r*nodalRho*p_vrtm[nDim*ic+j];
p_dpdxIp[j] += p_dndx[offSetDnDx+j]*nodalPressure;
lhsfac += -p_dndx_lhs[offSetDnDx+j]*p_scs_areav[ip*nDim+j];
}
// assemble to lhs; left
p_lhs[rowL+ic] += lhsfac;
// assemble to lhs; right
p_lhs[rowR+ic] -= lhsfac;
}
// assemble mdot
double mdot = 0.0;
for ( int j = 0; j < nDim; ++j ) {
mdot += (interpTogether*p_rho_uIp[j] + om_interpTogether*rhoIp*p_uIp[j]
- projTimeScale*(p_dpdxIp[j] - p_GpdxIp[j]))*p_scs_areav[ip*nDim+j];
}
// residual; left and right
p_rhs[il] -= mdot/projTimeScale;
p_rhs[ir] += mdot/projTimeScale;
}
// call supplemental
for ( size_t i = 0; i < supplementalAlgSize; ++i )
supplementalAlg_[i]->elem_execute( &lhs[0], &rhs[0], elem, meSCS, meSCV);
apply_coeff(connected_nodes, rhs, lhs, __FILE__);
}
}
}
//--------------------------------------------------------------------------
//-------- clip_min_distance_to_wall ---------------------------------------
//--------------------------------------------------------------------------
void
ShearStressTransportEquationSystem::clip_min_distance_to_wall()
{
// if this is a restart, then min distance has already been clipped
if (realm_.restarted_simulation())
return;
// okay, no restart: proceed with clipping of minimum wall distance
stk::mesh::BulkData & bulk_data = realm_.bulk_data();
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
// extract fields required
GenericFieldType *exposedAreaVec = meta_data.get_field<GenericFieldType>(meta_data.side_rank(), "exposed_area_vector");
VectorFieldType *coordinates = meta_data.get_field<VectorFieldType>(stk::topology::NODE_RANK, realm_.get_coordinates_name());
// define vector of parent topos; should always be UNITY in size
std::vector<stk::topology> parentTopo;
// selector
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
&stk::mesh::selectUnion(wallBcPart_);
stk::mesh::BucketVector const& face_buckets =
realm_.get_buckets( meta_data.side_rank(), s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = face_buckets.begin();
ib != face_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
// extract connected element topology
b.parent_topology(stk::topology::ELEMENT_RANK, parentTopo);
ThrowAssert ( parentTopo.size() == 1 );
stk::topology theElemTopo = parentTopo[0];
// extract master element
MasterElement *meSCS = realm_.get_surface_master_element(theElemTopo);
// face master element
const int nodesPerFace = b.topology().num_nodes();
std::vector<int> face_node_ordinal_vec(nodesPerFace);
const stk::mesh::Bucket::size_type length = b.size();
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// get face
stk::mesh::Entity face = b[k];
int num_face_nodes = bulk_data.num_nodes(face);
// pointer to face data
const double * areaVec = stk::mesh::field_data(*exposedAreaVec, face);
// extract the connected element to this exposed face; should be single in size!
const stk::mesh::Entity* face_elem_rels = bulk_data.begin_elements(face);
ThrowAssert( bulk_data.num_elements(face) == 1 );
// get element; its face ordinal number and populate face_node_ordinal_vec
stk::mesh::Entity element = face_elem_rels[0];
const int face_ordinal = bulk_data.begin_element_ordinals(face)[0];
theElemTopo.side_node_ordinals(face_ordinal, face_node_ordinal_vec.begin());
// get the relations off of element
stk::mesh::Entity const * elem_node_rels = bulk_data.begin_nodes(element);
// loop over face nodes
for ( int ip = 0; ip < num_face_nodes; ++ip ) {
const int offSetAveraVec = ip*nDim;
const int opposingNode = meSCS->opposingNodes(face_ordinal,ip);
const int nearestNode = face_node_ordinal_vec[ip];
// left and right nodes; right is on the face; left is the opposing node
stk::mesh::Entity nodeL = elem_node_rels[opposingNode];
stk::mesh::Entity nodeR = elem_node_rels[nearestNode];
// extract nodal fields
const double * coordL = stk::mesh::field_data(*coordinates, nodeL );
const double * coordR = stk::mesh::field_data(*coordinates, nodeR );
double aMag = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double axj = areaVec[offSetAveraVec+j];
aMag += axj*axj;
}
aMag = std::sqrt(aMag);
// form unit normal and determine yp (approximated by 1/4 distance along edge)
double ypbip = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double nj = areaVec[offSetAveraVec+j]/aMag;
const double ej = 0.25*(coordR[j] - coordL[j]);
ypbip += nj*ej*nj*ej;
}
ypbip = std::sqrt(ypbip);
// assemble to nodal quantities
double *minD = stk::mesh::field_data(*minDistanceToWall_, nodeR );
*minD = std::max(*minD, ypbip);
}
}
}
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleScalarElemOpenSolverAlgorithm::execute()
{
stk::mesh::BulkData & bulk_data = realm_.bulk_data();
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
const double small = 1.0e-16;
// extract user advection options (allow to potentially change over time)
const std::string dofName = scalarQ_->name();
const double alphaUpw = realm_.get_alpha_upw_factor(dofName);
const double hoUpwind = realm_.get_upw_factor(dofName);
// one minus flavor..
const double om_alphaUpw = 1.0-alphaUpw;
// space for LHS/RHS; nodesPerElement*nodesPerElement and nodesPerElement
std::vector<double> lhs;
std::vector<double> rhs;
std::vector<int> scratchIds;
std::vector<double> scratchVals;
std::vector<stk::mesh::Entity> connected_nodes;
// ip values; only boundary
std::vector<double> coordBip(nDim);
// pointers to fixed values
double *p_coordBip = &coordBip[0];
// nodal fields to gather
std::vector<double> ws_face_coordinates;
std::vector<double> ws_scalarQNp1;
std::vector<double> ws_bcScalarQ;
// master element
std::vector<double> ws_face_shape_function;
// deal with state
ScalarFieldType &scalarQNp1 = scalarQ_->field_of_state(stk::mesh::StateNP1);
ScalarFieldType &densityNp1 = density_->field_of_state(stk::mesh::StateNP1);
// define vector of parent topos; should always be UNITY in size
std::vector<stk::topology> parentTopo;
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
&stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& face_buckets =
realm_.get_buckets( meta_data.side_rank(), s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = face_buckets.begin();
ib != face_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
// extract connected element topology
b.parent_topology(stk::topology::ELEMENT_RANK, parentTopo);
ThrowAssert ( parentTopo.size() == 1 );
stk::topology theElemTopo = parentTopo[0];
// volume master element
MasterElement *meSCS = realm_.get_surface_master_element(theElemTopo);
const int nodesPerElement = meSCS->nodesPerElement_;
// face master element
MasterElement *meFC = realm_.get_surface_master_element(b.topology());
const int nodesPerFace = meFC->nodesPerElement_;
const int numScsBip = meFC->numIntPoints_;
std::vector<int> face_node_ordinal_vec(nodesPerFace);
// resize some things; matrix related
const int lhsSize = nodesPerElement*nodesPerElement;
const int rhsSize = nodesPerElement;
lhs.resize(lhsSize);
rhs.resize(rhsSize);
scratchIds.resize(rhsSize);
scratchVals.resize(rhsSize);
connected_nodes.resize(nodesPerElement);
// algorithm related; element
ws_face_coordinates.resize(nodesPerFace*nDim);
ws_scalarQNp1.resize(nodesPerFace);
ws_bcScalarQ.resize(nodesPerFace);
ws_face_shape_function.resize(numScsBip*nodesPerFace);
// pointers
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
double *p_face_coordinates = &ws_face_coordinates[0];
double *p_scalarQNp1 = &ws_scalarQNp1[0];
double *p_bcScalarQ = &ws_bcScalarQ[0];
double *p_face_shape_function = &ws_face_shape_function[0];
// shape functions
meFC->shape_fcn(&p_face_shape_function[0]);
const stk::mesh::Bucket::size_type length = b.size();
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// zero lhs/rhs
for ( int p = 0; p < lhsSize; ++p )
p_lhs[p] = 0.0;
for ( int p = 0; p < rhsSize; ++p )
p_rhs[p] = 0.0;
// get face
stk::mesh::Entity face = b[k];
// pointer to face data
const double * mdot = stk::mesh::field_data(*openMassFlowRate_, face);
//======================================
// gather nodal data off of face
//======================================
stk::mesh::Entity const * face_node_rels = bulk_data.begin_nodes(face);
int num_face_nodes = bulk_data.num_nodes(face);
// sanity check on num nodes
ThrowAssert( num_face_nodes == nodesPerFace );
for ( int ni = 0; ni < num_face_nodes; ++ni ) {
stk::mesh::Entity node = face_node_rels[ni];
// gather scalars
p_scalarQNp1[ni] = *stk::mesh::field_data(scalarQNp1, node);
p_bcScalarQ[ni] = *stk::mesh::field_data(*bcScalarQ_, node);
// gather vectors
double * coords = stk::mesh::field_data(*coordinates_, node);
const int offSet = ni*nDim;
for ( int i=0; i < nDim; ++i ) {
p_face_coordinates[offSet+i] = coords[i];
}
}
// extract the connected element to this exposed face; should be single in size!
const stk::mesh::Entity* face_elem_rels = bulk_data.begin_elements(face);
ThrowAssert( bulk_data.num_elements(face) == 1 );
// get element; its face ordinal number and populate face_node_ordinal_vec
stk::mesh::Entity element = face_elem_rels[0];
const int face_ordinal = bulk_data.begin_element_ordinals(face)[0];
theElemTopo.side_node_ordinals(face_ordinal, face_node_ordinal_vec.begin());
// mapping from ip to nodes for this ordinal
const int *ipNodeMap = meSCS->ipNodeMap(face_ordinal);
//==========================================
// gather nodal data off of element; n/a
//==========================================
stk::mesh::Entity const * elem_node_rels = bulk_data.begin_nodes(element);
int num_nodes = bulk_data.num_nodes(element);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
// set connected nodes
connected_nodes[ni] = elem_node_rels[ni];
}
// loop over face nodes
for ( int ip = 0; ip < numScsBip; ++ip ) {
const int opposingNode = meSCS->opposingNodes(face_ordinal,ip);
const int nearestNode = ipNodeMap[ip];
const int offSetSF_face = ip*nodesPerFace;
// left and right nodes; right is on the face; left is the opposing node
stk::mesh::Entity nodeL = elem_node_rels[opposingNode];
stk::mesh::Entity nodeR = elem_node_rels[nearestNode];
// zero out vector quantities
for ( int j = 0; j < nDim; ++j )
p_coordBip[j] = 0.0;
// interpolate to bip
double qIp = 0.0;
double qIpEntrain = 0.0;
for ( int ic = 0; ic < nodesPerFace; ++ic ) {
const double r = p_face_shape_function[offSetSF_face+ic];
qIp += r*p_scalarQNp1[ic];
qIpEntrain += r*p_bcScalarQ[ic];
const int offSetFN = ic*nDim;
for ( int j = 0; j < nDim; ++j ) {
p_coordBip[j] += r*p_face_coordinates[offSetFN+j];
}
}
// Peclet factor; along the edge is fine
const double densL = *stk::mesh::field_data(densityNp1, nodeL);
const double densR = *stk::mesh::field_data(densityNp1, nodeR);
const double diffCoeffL = *stk::mesh::field_data(*diffFluxCoeff_, nodeL);
const double diffCoeffR = *stk::mesh::field_data(*diffFluxCoeff_, nodeR);
const double scalarQNp1R = *stk::mesh::field_data(scalarQNp1, nodeR);
const double *vrtmL = stk::mesh::field_data(*velocityRTM_, nodeL);
const double *vrtmR = stk::mesh::field_data(*velocityRTM_, nodeR);
const double *coordL = stk::mesh::field_data(*coordinates_, nodeL);
const double *coordR = stk::mesh::field_data(*coordinates_, nodeR);
const double *dqdxR = stk::mesh::field_data(*dqdx_, nodeR);
double udotx = 0.0;
double dqR = 0.0;
for ( int i = 0; i < nDim; ++i ) {
const double dxi = coordR[i] - coordL[i];
udotx += 0.5*dxi*(vrtmL[i] + vrtmR[i]);
// extrapolation
const double dx_bip = coordBip[i] - coordR[i];
dqR += dx_bip*dqdxR[i]*hoUpwind;
}
const double qIpUpw = scalarQNp1R + dqR;
const double diffIp = 0.5*(diffCoeffL/densL + diffCoeffR/densR);
const double pecfac = pecletFunction_->execute(std::abs(udotx)/(diffIp+small));
const double om_pecfac = 1.0-pecfac;
//================================
// advection first (and only)
//================================
const double tmdot = mdot[ip];
const int rowR = nearestNode*nodesPerElement;
// advection; leaving the domain
if ( tmdot > 0.0 ) {
// central; is simply qIp
// upwind
const double qUpwind = alphaUpw*qIpUpw + (om_alphaUpw)*qIp;
// total advection
const double aflux = tmdot*(pecfac*qUpwind+om_pecfac*qIp);
p_rhs[nearestNode] -= aflux;
// upwind lhs
p_lhs[rowR+nearestNode] += tmdot*pecfac*alphaUpw;
// central part
const double fac = tmdot*(pecfac*om_alphaUpw+om_pecfac);
for ( int ic = 0; ic < nodesPerFace; ++ic ) {
const double r = p_face_shape_function[offSetSF_face+ic];
const int nn = face_node_ordinal_vec[ic];
p_lhs[rowR+nn] += r*fac;
}
}
else {
// extrainment; advect in from specified value
const double aflux = tmdot*qIpEntrain;
p_rhs[nearestNode] -= aflux;
}
}
apply_coeff(connected_nodes, scratchIds, scratchVals, rhs, lhs, __FILE__);
}
}
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleScalarElemSolverAlgorithm::execute()
{
stk::mesh::BulkData & bulk_data = realm_.bulk_data();
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
const double small = 1.0e-16;
// extract user advection options (allow to potentially change over time)
const std::string dofName = scalarQ_->name();
const double hybridFactor = realm_.get_hybrid_factor(dofName);
const double alpha = realm_.get_alpha_factor(dofName);
const double alphaUpw = realm_.get_alpha_upw_factor(dofName);
const double hoUpwind = realm_.get_upw_factor(dofName);
const bool useLimiter = realm_.primitive_uses_limiter(dofName);
// one minus flavor..
const double om_alpha = 1.0-alpha;
const double om_alphaUpw = 1.0-alphaUpw;
// space for LHS/RHS; nodesPerElem*nodesPerElem* and nodesPerElem
std::vector<double> lhs;
std::vector<double> rhs;
std::vector<stk::mesh::Entity> connected_nodes;
// supplemental algorithm size and setup
const size_t supplementalAlgSize = supplementalAlg_.size();
for ( size_t i = 0; i < supplementalAlgSize; ++i )
supplementalAlg_[i]->setup();
// nodal fields to gather
std::vector<double> ws_velocityNp1;
std::vector<double> ws_meshVelocity;
std::vector<double> ws_vrtm;
std::vector<double> ws_coordinates;
std::vector<double> ws_scalarQNp1;
std::vector<double> ws_dqdx;
std::vector<double> ws_density;
std::vector<double> ws_diffFluxCoeff;
// geometry related to populate
std::vector<double> ws_scs_areav;
std::vector<double> ws_dndx;
std::vector<double> ws_deriv;
std::vector<double> ws_det_j;
std::vector<double> ws_shape_function;
// ip values
std::vector<double>coordIp(nDim);
// pointers
double *p_coordIp = &coordIp[0];
// deal with state
ScalarFieldType &scalarQNp1 = scalarQ_->field_of_state(stk::mesh::StateNP1);
VectorFieldType &velocityNp1 = velocity_->field_of_state(stk::mesh::StateNP1);
ScalarFieldType &densityNp1 = density_->field_of_state(stk::mesh::StateNP1);
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
&stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& elem_buckets =
realm_.get_buckets( stk::topology::ELEMENT_RANK, s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = elem_buckets.begin();
ib != elem_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
const stk::mesh::Bucket::size_type length = b.size();
// extract master element
MasterElement *meSCS = realm_.get_surface_master_element(b.topology());
// extract master element specifics
const int nodesPerElement = meSCS->nodesPerElement_;
const int numScsIp = meSCS->numIntPoints_;
const int *lrscv = meSCS->adjacentNodes();
// resize some things; matrix related
const int lhsSize = nodesPerElement*nodesPerElement;
const int rhsSize = nodesPerElement;
lhs.resize(lhsSize);
rhs.resize(rhsSize);
connected_nodes.resize(nodesPerElement);
// algorithm related
ws_velocityNp1.resize(nodesPerElement*nDim);
ws_meshVelocity.resize(nodesPerElement*nDim);
ws_vrtm.resize(nodesPerElement*nDim);
ws_coordinates.resize(nodesPerElement*nDim);
ws_dqdx.resize(nodesPerElement*nDim);
ws_scalarQNp1.resize(nodesPerElement);
ws_density.resize(nodesPerElement);
ws_diffFluxCoeff.resize(nodesPerElement);
ws_scs_areav.resize(numScsIp*nDim);
ws_dndx.resize(nDim*numScsIp*nodesPerElement);
ws_deriv.resize(nDim*numScsIp*nodesPerElement);
ws_det_j.resize(numScsIp);
ws_shape_function.resize(numScsIp*nodesPerElement);
// pointer to lhs/rhs
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
double *p_velocityNp1 = &ws_velocityNp1[0];
double *p_meshVelocity = &ws_meshVelocity[0];
double *p_vrtm = &ws_vrtm[0];
double *p_coordinates = &ws_coordinates[0];
double *p_dqdx = &ws_dqdx[0];
double *p_scalarQNp1 = &ws_scalarQNp1[0];
double *p_density = &ws_density[0];
double *p_diffFluxCoeff = &ws_diffFluxCoeff[0];
double *p_scs_areav = &ws_scs_areav[0];
double *p_dndx = &ws_dndx[0];
double *p_shape_function = &ws_shape_function[0];
// extract shape function
meSCS->shape_fcn(&p_shape_function[0]);
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// get elem
stk::mesh::Entity elem = b[k];
// zero lhs/rhs
for ( int p = 0; p < lhsSize; ++p )
p_lhs[p] = 0.0;
for ( int p = 0; p < rhsSize; ++p )
p_rhs[p] = 0.0;
// ip data for this element; scs and scv
const double *mdot = stk::mesh::field_data(*massFlowRate_, elem );
//===============================================
// gather nodal data; this is how we do it now..
//===============================================
stk::mesh::Entity const * node_rels = bulk_data.begin_nodes(elem);
int num_nodes = bulk_data.num_nodes(elem);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
stk::mesh::Entity node = node_rels[ni];
// set connected nodes
connected_nodes[ni] = node;
// pointers to real data
const double * uNp1 = stk::mesh::field_data(velocityNp1, node );
const double * vNp1 = stk::mesh::field_data(*meshVelocity_, node);
const double * coords = stk::mesh::field_data(*coordinates_, node );
const double * dq = stk::mesh::field_data(*dqdx_, node );
// gather scalars
p_scalarQNp1[ni] = *stk::mesh::field_data(scalarQNp1, node );
p_density[ni] = *stk::mesh::field_data(densityNp1, node );
p_diffFluxCoeff[ni] = *stk::mesh::field_data(*diffFluxCoeff_, node );
// gather vectors
const int niNdim = ni*nDim;
for ( int i=0; i < nDim; ++i ) {
p_velocityNp1[niNdim+i] = uNp1[i];
p_vrtm[niNdim+i] = uNp1[i];
p_meshVelocity[niNdim+i] = vNp1[i];
p_coordinates[niNdim+i] = coords[i];
p_dqdx[niNdim+i] = dq[i];
}
}
// compute geometry
double scs_error = 0.0;
meSCS->determinant(1, &p_coordinates[0], &p_scs_areav[0], &scs_error);
// compute dndx
meSCS->grad_op(1, &p_coordinates[0], &p_dndx[0], &ws_deriv[0], &ws_det_j[0], &scs_error);
// manage velocity relative to mesh
if ( meshMotion_ ) {
const int kSize = num_nodes*nDim;
for ( int k = 0; k < kSize; ++k ) {
p_vrtm[k] -= p_meshVelocity[k];
}
}
for ( int ip = 0; ip < numScsIp; ++ip ) {
// left and right nodes for this ip
const int il = lrscv[2*ip];
const int ir = lrscv[2*ip+1];
// corresponding matrix rows
const int rowL = il*nodesPerElement;
const int rowR = ir*nodesPerElement;
// save off mdot
const double tmdot = mdot[ip];
// zero out values of interest for this ip
for ( int j = 0; j < nDim; ++j ) {
p_coordIp[j] = 0.0;
}
// save off ip values; offset to Shape Function
double rhoIp = 0.0;
double muIp = 0.0;
double qIp = 0.0;
const int offSetSF = ip*nodesPerElement;
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
const double r = p_shape_function[offSetSF+ic];
rhoIp += r*p_density[ic];
muIp += r*p_diffFluxCoeff[ic];
qIp += r*p_scalarQNp1[ic];
// compute scs point values
for ( int i = 0; i < nDim; ++i ) {
p_coordIp[i] += r*p_coordinates[ic*nDim+i];
}
}
// Peclet factor; along the edge
const double diffIp = 0.5*(p_diffFluxCoeff[il]/p_density[il]
+ p_diffFluxCoeff[ir]/p_density[ir]);
double udotx = 0.0;
for(int j = 0; j < nDim; ++j ) {
const double dxj = p_coordinates[ir*nDim+j]-p_coordinates[il*nDim+j];
const double uj = 0.5*(p_vrtm[il*nDim+j] + p_vrtm[ir*nDim+j]);
udotx += uj*dxj;
}
double pecfac = hybridFactor*udotx/(diffIp+small);
pecfac = pecfac*pecfac/(5.0 + pecfac*pecfac);
const double om_pecfac = 1.0-pecfac;
// left and right extrapolation
double dqL = 0.0;
double dqR = 0.0;
for(int j = 0; j < nDim; ++j ) {
const double dxjL = p_coordIp[j] - p_coordinates[il*nDim+j];
const double dxjR = p_coordinates[ir*nDim+j] - p_coordIp[j];
dqL += dxjL*p_dqdx[nDim*il+j];
dqR += dxjR*p_dqdx[nDim*ir+j];
}
// add limiter if appropriate
double limitL = 1.0;
double limitR = 1.0;
if ( useLimiter ) {
const double dq = p_scalarQNp1[ir] - p_scalarQNp1[il];
const double dqMl = 2.0*2.0*dqL - dq;
const double dqMr = 2.0*2.0*dqR - dq;
limitL = van_leer(dqMl, dq, small);
limitR = van_leer(dqMr, dq, small);
}
// extrapolated; for now limit (along edge is fine)
const double qIpL = p_scalarQNp1[il] + dqL*hoUpwind*limitL;
const double qIpR = p_scalarQNp1[ir] - dqR*hoUpwind*limitR;
// assemble advection; rhs and upwind contributions
// 2nd order central; simply qIp from above
// upwind
const double qUpwind = (tmdot > 0) ? alphaUpw*qIpL + om_alphaUpw*qIp
: alphaUpw*qIpR + om_alphaUpw*qIp;
// generalized central (2nd and 4th order)
const double qHatL = alpha*qIpL + om_alpha*qIp;
const double qHatR = alpha*qIpR + om_alpha*qIp;
const double qCds = 0.5*(qHatL + qHatR);
// total advection
const double aflux = tmdot*(pecfac*qUpwind + om_pecfac*qCds);
// right hand side; L and R
p_rhs[il] -= aflux;
p_rhs[ir] += aflux;
// advection operator sens; all but central
// upwind advection (includes 4th); left node
const double alhsfacL = 0.5*(tmdot+std::abs(tmdot))*pecfac*alphaUpw
+ 0.5*alpha*om_pecfac*tmdot;
p_lhs[rowL+il] += alhsfacL;
p_lhs[rowR+il] -= alhsfacL;
// upwind advection; right node
const double alhsfacR = 0.5*(tmdot-std::abs(tmdot))*pecfac*alphaUpw
+ 0.5*alpha*om_pecfac*tmdot;
p_lhs[rowR+ir] -= alhsfacR;
p_lhs[rowL+ir] += alhsfacR;
double qDiff = 0.0;
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
// shape function
const double r = p_shape_function[offSetSF+ic];
// upwind (il/ir) handled above; collect terms on alpha and alphaUpw
const double lhsfacAdv = r*tmdot*(pecfac*om_alphaUpw + om_pecfac*om_alpha);
// advection operator lhs; rhs handled above
// lhs; il then ir
p_lhs[rowL+ic] += lhsfacAdv;
p_lhs[rowR+ic] -= lhsfacAdv;
// diffusion
double lhsfacDiff = 0.0;
const int offSetDnDx = nDim*nodesPerElement*ip + ic*nDim;
for ( int j = 0; j < nDim; ++j ) {
lhsfacDiff += -muIp*p_dndx[offSetDnDx+j]*p_scs_areav[ip*nDim+j];
}
qDiff += lhsfacDiff*p_scalarQNp1[ic];
// lhs; il then ir
p_lhs[rowL+ic] += lhsfacDiff;
p_lhs[rowR+ic] -= lhsfacDiff;
}
// rhs; il then ir
p_rhs[il] -= qDiff;
p_rhs[ir] += qDiff;
}
// call supplemental
for ( size_t i = 0; i < supplementalAlgSize; ++i )
supplementalAlg_[i]->elem_execute( nodesPerElement, numScsIp, &lhs[0], &rhs[0], elem);
apply_coeff(connected_nodes, rhs, lhs, __FILE__);
}
}
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleScalarEdgeOpenSolverAlgorithm::execute()
{
stk::mesh::BulkData & bulk_data = realm_.bulk_data();
stk::mesh::MetaData & meta_data = realm_.meta_data();
// space for LHS/RHS; nodesPerElement*nodesPerElement and nodesPerElement
std::vector<double> lhs;
std::vector<double> rhs;
std::vector<stk::mesh::Entity> connected_nodes;
// deal with state
ScalarFieldType &scalarQNp1 = scalarQ_->field_of_state(stk::mesh::StateNP1);
// define vector of parent topos; should always be UNITY in size
std::vector<stk::topology> parentTopo;
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
&stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& face_buckets =
realm_.get_buckets( meta_data.side_rank(), s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = face_buckets.begin();
ib != face_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
// extract connected element topology
b.parent_topology(stk::topology::ELEMENT_RANK, parentTopo);
ThrowAssert ( parentTopo.size() == 1 );
stk::topology theElemTopo = parentTopo[0];
// volume master element
MasterElement *meSCS = realm_.get_surface_master_element(theElemTopo);
const int nodesPerElement = meSCS->nodesPerElement_;
// face master element
MasterElement *meFC = realm_.get_surface_master_element(b.topology());
const int nodesPerFace = meFC->nodesPerElement_;
std::vector<int> face_node_ordinal_vec(nodesPerFace);
// resize some things; matrix related
const int lhsSize = nodesPerElement*nodesPerElement;
const int rhsSize = nodesPerElement;
lhs.resize(lhsSize);
rhs.resize(rhsSize);
connected_nodes.resize(nodesPerElement);
// pointers
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
// size some things that are useful
const int num_face_nodes = b.topology().num_nodes();
std::vector<int> face_node_ordinals(num_face_nodes);
const stk::mesh::Bucket::size_type length = b.size();
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// zero lhs/rhs
for ( int p = 0; p < lhsSize; ++p )
p_lhs[p] = 0.0;
for ( int p = 0; p < rhsSize; ++p )
p_rhs[p] = 0.0;
// get face
stk::mesh::Entity face = b[k];
// pointer to face data
const double * mdot = stk::mesh::field_data(*openMassFlowRate_, face);
// extract the connected element to this exposed face; should be single in size!
const stk::mesh::Entity* face_elem_rels = bulk_data.begin_elements(face);
ThrowAssert( bulk_data.num_elements(face) == 1 );
// get element; its face ordinal number and populate face_node_ordinal_vec
stk::mesh::Entity element = face_elem_rels[0];
const int face_ordinal = bulk_data.begin_element_ordinals(face)[0];
theElemTopo.side_node_ordinals(face_ordinal, face_node_ordinal_vec.begin());
//==========================================
// gather nodal data off of element; n/a
//==========================================
const stk::mesh::Entity* elem_node_rels = bulk_data.begin_nodes(element);
const int num_nodes = bulk_data.num_nodes(element);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
stk::mesh::Entity node = elem_node_rels[ni];
// set connected nodes
connected_nodes[ni] = node;
}
// loop over face nodes
for ( int ip = 0; ip < num_face_nodes; ++ip ) {
const int nearestNode = face_node_ordinal_vec[ip];
// left and right nodes; right is on the face; left is the opposing node
stk::mesh::Entity nodeR = elem_node_rels[nearestNode];
const double qR = *stk::mesh::field_data( scalarQNp1, nodeR );
const double qEntrain = *stk::mesh::field_data( *bcScalarQ_, nodeR );
//================================
// advection first (and only)
//================================
const double tmdot = mdot[ip];
const int rowR = nearestNode*nodesPerElement;
// advection; leaving the domain
if ( tmdot > 0.0 ) {
// total advection
const double aflux = tmdot*qR;
p_rhs[nearestNode] -= aflux;
// upwind lhs
p_lhs[rowR+nearestNode] += tmdot;
}
else {
// extrainment; advect in from specified value
const double aflux = tmdot*qEntrain;
p_rhs[nearestNode] -= aflux;
}
}
apply_coeff(connected_nodes, rhs, lhs, __FILE__);
}
}
}
//--------------------------------------------------------------------------
//-------- elem_execute ----------------------------------------------------
//--------------------------------------------------------------------------
void
ScalarMassBDF2ElemSuppAlg::elem_execute(
double *lhs,
double *rhs,
stk::mesh::Entity element,
MasterElement */*meSCS*/,
MasterElement *meSCV)
{
// pointer to ME methods
const int *ipNodeMap = meSCV->ipNodeMap();
const int nodesPerElement = meSCV->nodesPerElement_;
const int numScvIp = meSCV->numIntPoints_;
// gather
stk::mesh::Entity const * node_rels = bulkData_->begin_nodes(element);
int num_nodes = bulkData_->num_nodes(element);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
stk::mesh::Entity node = node_rels[ni];
// pointers to real data
const double * coords = stk::mesh::field_data(*coordinates_, node);
// gather scalars
ws_qNm1_[ni] = *stk::mesh::field_data(*scalarQNm1_, node);
ws_qN_[ni] = *stk::mesh::field_data(*scalarQN_, node);
ws_qNp1_[ni] = *stk::mesh::field_data(*scalarQNp1_, node);
ws_rhoNm1_[ni] = *stk::mesh::field_data(*densityNm1_, node);
ws_rhoN_[ni] = *stk::mesh::field_data(*densityN_, node);
ws_rhoNp1_[ni] = *stk::mesh::field_data(*densityNp1_, node);
// gather vectors
const int niNdim = ni*nDim_;
for ( int i=0; i < nDim_; ++i ) {
ws_coordinates_[niNdim+i] = coords[i];
}
}
// compute geometry
double scv_error = 0.0;
meSCV->determinant(1, &ws_coordinates_[0], &ws_scv_volume_[0], &scv_error);
for ( int ip = 0; ip < numScvIp; ++ip ) {
// nearest node to ip
const int nearestNode = ipNodeMap[ip];
// zero out; scalar
double qNm1Scv = 0.0;
double qNScv = 0.0;
double qNp1Scv = 0.0;
double rhoNm1Scv = 0.0;
double rhoNScv = 0.0;
double rhoNp1Scv = 0.0;
const int offSet = ip*nodesPerElement;
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
// save off shape function
const double r = ws_shape_function_[offSet+ic];
// scalar q
qNm1Scv += r*ws_qNm1_[ic];
qNScv += r*ws_qN_[ic];
qNp1Scv += r*ws_qNp1_[ic];
// density
rhoNm1Scv += r*ws_rhoNm1_[ic];
rhoNScv += r*ws_rhoN_[ic];
rhoNp1Scv += r*ws_rhoNp1_[ic];
}
// assemble rhs
const double scV = ws_scv_volume_[ip];
rhs[nearestNode] +=
-(gamma1_*rhoNp1Scv*qNp1Scv + gamma2_*rhoNScv*qNScv + gamma3_*rhoNm1Scv*qNm1Scv)*scV/dt_;
// manage LHS
for ( int ic = 0; ic < nodesPerElement; ++ic ) {
// save off shape function
const double r = ws_shape_function_[offSet+ic];
const double lhsfac = r*gamma1_*rhoNp1Scv*scV/dt_;
const int rNNiC = nearestNode*nodesPerElement+ic;
lhs[rNNiC] += lhsfac;
}
}
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleMomentumEdgeOpenSolverAlgorithm::execute()
{
stk::mesh::BulkData & bulk_data = realm_.bulk_data();
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
// nearest face entrainment
const double nfEntrain = realm_.solutionOptions_->nearestFaceEntrain_;
const double om_nfEntrain = 1.0-nfEntrain;
// space for dui/dxj; the modified gradient with NOC
std::vector<double> duidxj(nDim*nDim);
// lhs/rhs space
std::vector<stk::mesh::Entity> connected_nodes;
std::vector<double> rhs;
std::vector<double> lhs;
std::vector<double> nx(nDim);
std::vector<double> fx(nDim);
// pointers
double *p_duidxj = &duidxj[0];
double *p_nx = &nx[0];
double *p_fx = &fx[0];
// deal with state
VectorFieldType &velocityNp1 = velocity_->field_of_state(stk::mesh::StateNP1);
// define vector of parent topos
std::vector<stk::topology> parentTopo;
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
&stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& face_buckets =
realm_.get_buckets( meta_data.side_rank(), s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = face_buckets.begin();
ib != face_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
// extract connected element topology
b.parent_topology(stk::topology::ELEMENT_RANK, parentTopo);
ThrowAssert ( parentTopo.size() == 1 );
stk::topology theElemTopo = parentTopo[0];
MasterElement *meSCS = realm_.get_surface_master_element(theElemTopo);
const int nodesPerElement = meSCS->nodesPerElement_;
// resize some things; matrix related
const int lhsSize = nodesPerElement*nDim*nodesPerElement*nDim;
const int rhsSize = nodesPerElement*nDim;
lhs.resize(lhsSize);
rhs.resize(rhsSize);
connected_nodes.resize(nodesPerElement);
// pointer to lhs/rhs
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
// size some things that are useful
const int num_face_nodes = b.topology().num_nodes();
std::vector<int> face_node_ordinals(num_face_nodes);
const stk::mesh::Bucket::size_type length = b.size();
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// zero lhs/rhs
for ( int p = 0; p < lhsSize; ++p )
p_lhs[p] = 0.0;
for ( int p = 0; p < rhsSize; ++p )
p_rhs[p] = 0.0;
// pointer to face data
const double * areaVec = stk::mesh::field_data(*exposedAreaVec_, b, k);
const double * mdot = stk::mesh::field_data(*openMassFlowRate_, b, k);
// extract the connected element to this exposed face; should be single in size!
stk::mesh::Entity const * face_elem_rels = b.begin_elements(k);
ThrowAssert( b.num_elements(k) == 1 );
// get element; its face ordinal number and populate face_node_ordinals
stk::mesh::Entity element = face_elem_rels[0];
const int face_ordinal = b.begin_element_ordinals(k)[0];
theElemTopo.side_node_ordinals(face_ordinal, face_node_ordinals.begin());
// get the relations; populate connected nodes
stk::mesh::Entity const * elem_node_rels = bulk_data.begin_nodes(element);
int num_nodes = bulk_data.num_nodes(element);
// sanity check on num nodes
ThrowAssert( num_nodes == nodesPerElement );
for ( int ni = 0; ni < num_nodes; ++ni ) {
// set connected nodes
connected_nodes[ni] = elem_node_rels[ni];
}
// loop over face nodes (maps directly to ips)
for ( int ip = 0; ip < num_face_nodes; ++ip ) {
const int opposingNode = meSCS->opposingNodes(face_ordinal,ip); // "Left"
const int nearestNode = face_node_ordinals[ip]; // "Right"
// left and right nodes; right is on the face; left is the opposing node
stk::mesh::Entity nodeL = elem_node_rels[opposingNode];
stk::mesh::Entity nodeR = elem_node_rels[nearestNode];
// extract nodal fields
const double * coordL = stk::mesh::field_data(*coordinates_, nodeL );
const double * coordR = stk::mesh::field_data(*coordinates_, nodeR );
const double * uNp1L = stk::mesh::field_data(velocityNp1, nodeL );
const double * uNp1R = stk::mesh::field_data(velocityNp1, nodeR );
const double viscosityR = *stk::mesh::field_data(*viscosity_, nodeR );
const double viscBip = viscosityR;
// a few only required (or even defined) on nodeR
const double *bcVelocity = stk::mesh::field_data(*velocityBc_, nodeR );
const double * dudxR = stk::mesh::field_data(*dudx_, nodeR );
// offset for bip area vector
const int faceOffSet = ip*nDim;
// compute geometry
double axdx = 0.0;
double asq = 0.0;
double udotx = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double axj = areaVec[faceOffSet+j];
const double dxj = coordR[j] - coordL[j];
asq += axj*axj;
axdx += axj*dxj;
udotx += 0.5*dxj*(uNp1L[j] + uNp1R[j]);
}
const double inv_axdx = 1.0/axdx;
const double amag = std::sqrt(asq);
// form duidxj with over-relaxed procedure of Jasak:
for ( int i = 0; i < nDim; ++i ) {
// difference between R and L nodes for component i
const double uidiff = uNp1R[i] - uNp1L[i];
// offset into all forms of dudx
const int offSetI = nDim*i;
// start sum for NOC contribution
double GlUidxl = 0.0;
for ( int l = 0; l< nDim; ++l ) {
const int offSetIL = offSetI+l;
const double dxl = coordR[l] - coordL[l];
const double GlUi = dudxR[offSetIL];
GlUidxl += GlUi*dxl;
}
// form full tensor dui/dxj with NOC
for ( int j = 0; j < nDim; ++j ) {
const int offSetIJ = offSetI+j;
const double axj = areaVec[faceOffSet+j];
const double GjUi = dudxR[offSetIJ];
p_duidxj[offSetIJ] = GjUi + (uidiff - GlUidxl)*axj*inv_axdx;
}
}
// divU
double divU = 0.0;
for ( int j = 0; j < nDim; ++j)
divU += p_duidxj[j*nDim+j];
double fxnx = 0.0;
double uxnx = 0.0;
double uxnxip = 0.0;
double uspecxnx = 0.0;
for (int i = 0; i < nDim; ++i ) {
const double axi = areaVec[faceOffSet+i];
double fxi = 2.0/3.0*viscBip*divU*axi*includeDivU_;
const int offSetI = nDim*i;
const double nxi = axi/amag;
for ( int j = 0; j < nDim; ++j ) {
const int offSetTrans = nDim*j+i;
const double axj = areaVec[faceOffSet+j];
fxi += -viscBip*(p_duidxj[offSetI+j] + p_duidxj[offSetTrans])*axj;
}
fxnx += nxi*fxi;
uxnx += nxi*uNp1R[i];
uxnxip += 0.5*nxi*(uNp1L[i]+uNp1R[i]);
uspecxnx += nxi*bcVelocity[i];
// save off normal and force for each component i
p_nx[i] = nxi;
p_fx[i] = fxi;
}
// full stress, sigma_ij
for (int i = 0; i < nDim; ++i ) {
// setup for matrix contribution assembly
const int indexL = opposingNode*nDim + i;
const int indexR = nearestNode*nDim + i;
const int rowR = indexR*nodesPerElement*nDim;
const int rRiL_i = rowR+indexL;
const int rRiR_i = rowR+indexR;
// subtract normal component
const double diffFlux = p_fx[i] - p_nx[i]*fxnx;
const double om_nxinxi = 1.0-p_nx[i]*p_nx[i];
p_rhs[indexR] -= diffFlux;
double lhsFac = -viscBip*asq*inv_axdx*om_nxinxi;
p_lhs[rRiL_i] -= lhsFac;
p_lhs[rRiR_i] += lhsFac;
const double axi = areaVec[faceOffSet+i];
for ( int j = 0; j < nDim; ++j ) {
const double axj = areaVec[faceOffSet+j];
lhsFac = -viscBip*axi*axj*inv_axdx*om_nxinxi;
const int colL = opposingNode*nDim + j;
const int colR = nearestNode*nDim + j;
const int rRiL_j = rowR+colL;
const int rRiR_j = rowR+colR;
p_lhs[rRiL_j] -= lhsFac;
p_lhs[rRiR_j] += lhsFac;
if ( i == j ) {
// nothing
}
else {
const double nxinxj = p_nx[i]*p_nx[j];
lhsFac = viscBip*asq*inv_axdx*nxinxj;
p_lhs[rRiL_j] -= lhsFac;
p_lhs[rRiR_j] += lhsFac;
lhsFac = viscBip*axj*axj*inv_axdx*nxinxj;
p_lhs[rRiL_j] -= lhsFac;
p_lhs[rRiR_j] += lhsFac;
lhsFac = viscBip*axj*axi*inv_axdx*nxinxj;
p_lhs[rRiL_i] -= lhsFac;
p_lhs[rRiR_i] += lhsFac;
}
}
}
// advection
const double tmdot = mdot[ip];
if ( tmdot > 0 ) {
// leaving the domain
for ( int i = 0; i < nDim; ++i ) {
// setup for matrix contribution assembly
const int indexR = nearestNode*nDim + i;
const int rowR = indexR*nodesPerElement*nDim;
const int rRiR = rowR+indexR;
p_rhs[indexR] -= tmdot*uNp1R[i];
p_lhs[rRiR] += tmdot;
}
}
else {
// entraining; constrain to be normal
for ( int i = 0; i < nDim; ++i ) {
// setup for matrix contribution assembly
const int indexR = nearestNode*nDim + i;
const int rowR = indexR*nodesPerElement*nDim;
// constrain to be normal
p_rhs[indexR] -= tmdot*(nfEntrain*uxnx + om_nfEntrain*uxnxip)*p_nx[i];
// user spec entrainment (tangential)
p_rhs[indexR] -= tmdot*(bcVelocity[i]-uspecxnx*p_nx[i]);
for ( int j = 0; j < nDim; ++j ) {
const int colL = opposingNode*nDim + j;
const int colR = nearestNode*nDim + j;
p_lhs[rowR+colR] += tmdot*(nfEntrain + om_nfEntrain*0.5)*p_nx[i]*p_nx[j];
p_lhs[rowR+colL] += tmdot*om_nfEntrain*0.5*p_nx[i]*p_nx[j];
}
}
}
}
apply_coeff(connected_nodes, rhs, lhs, __FILE__);
}
}
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
ComputeHeatTransferEdgeWallAlgorithm::execute()
{
stk::mesh::BulkData & bulk_data = realm_.bulk_data();
stk::mesh::MetaData & meta_data = realm_.meta_data();
const int nDim = meta_data.spatial_dimension();
const double dt = realm_.get_time_step();
// define vector of parent topos; should always be UNITY in size
std::vector<stk::topology> parentTopo;
// define some common selectors
stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
&stk::mesh::selectUnion(partVec_);
stk::mesh::BucketVector const& face_buckets =
realm_.get_buckets( meta_data.side_rank(), s_locally_owned_union );
for ( stk::mesh::BucketVector::const_iterator ib = face_buckets.begin();
ib != face_buckets.end() ; ++ib ) {
stk::mesh::Bucket & b = **ib ;
// extract connected element topology
b.parent_topology(stk::topology::ELEMENT_RANK, parentTopo);
ThrowAssert ( parentTopo.size() == 1 );
stk::topology theElemTopo = parentTopo[0];
MasterElement *meSCS = sierra::nalu::MasterElementRepo::get_surface_master_element(theElemTopo);
// size some things that are useful
const int num_face_nodes = b.topology().num_nodes();
const stk::mesh::Bucket::size_type length = b.size();
for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
// pointer to face data
const double * areaVec = stk::mesh::field_data(*exposedAreaVec_, b, k);
// extract the connected element to this exposed face; should be single in size!
stk::mesh::Entity const * face_elem_rels = b.begin_elements(k);
ThrowAssert( b.num_elements(k) == 1 );
// get element; its face ordinal number and populate face_node_ordinals
stk::mesh::Entity element = face_elem_rels[0];
const int face_ordinal = b.begin_element_ordinals(k)[0];
const int *face_node_ordinals = meSCS->side_node_ordinals(face_ordinal);
// get the relations
stk::mesh::Entity const * elem_node_rels = bulk_data.begin_nodes(element);
for ( int ip = 0; ip < num_face_nodes; ++ip ) {
const int opposingNode = meSCS->opposingNodes(face_ordinal,ip);
const int nearestNode = face_node_ordinals[ip];
// left and right nodes; right is on the face; left is the opposing node
stk::mesh::Entity nodeL = elem_node_rels[opposingNode];
stk::mesh::Entity nodeR = elem_node_rels[nearestNode];
// extract nodal fields
const double * coordL = stk::mesh::field_data(*coordinates_, nodeL );
const double * coordR = stk::mesh::field_data(*coordinates_, nodeR );
const double tempL = *stk::mesh::field_data(*temperature_, nodeL );
const double tempR = *stk::mesh::field_data(*temperature_, nodeR );
// nearest nodes; gathered and to-be-scattered
const double * dhdxR = stk::mesh::field_data(*dhdx_, nodeR );
const double densityR = *stk::mesh::field_data(*density_, nodeR );
const double thermalCondR = *stk::mesh::field_data(*thermalCond_, nodeR );
const double specificHeatR = *stk::mesh::field_data(*specificHeat_, nodeR );
double *assembledWallArea = stk::mesh::field_data(*assembledWallArea_, nodeR);
double *referenceTemperature = stk::mesh::field_data(*referenceTemperature_, nodeR);
double *heatTransferCoefficient = stk::mesh::field_data(*heatTransferCoefficient_, nodeR);
double *normalHeatFlux = stk::mesh::field_data(*normalHeatFlux_, nodeR);
double *robinCouplingParameter = stk::mesh::field_data(*robinCouplingParameter_, nodeR);
// offset for bip area vector
const int faceOffSet = ip*nDim;
// compute geometry
double axdx = 0.0;
double asq = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double axj = areaVec[faceOffSet+j];
const double dxj = coordR[j] - coordL[j];
asq += axj*axj;
axdx += axj*dxj;
}
const double inv_axdx = 1.0/axdx;
const double aMag = std::sqrt(asq);
const double edgeLen = axdx/aMag;
// NOC; convert dhdx to dTdx
double nonOrth = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double axj = areaVec[faceOffSet+j];
const double dxj = coordR[j] - coordL[j];
const double kxj = axj - asq*inv_axdx*dxj;
const double GjT = dhdxR[j]/specificHeatR;
nonOrth += -thermalCondR*kxj*GjT;
}
// compute coupling parameter
const double chi = densityR * specificHeatR * edgeLen * edgeLen
/ (2 * thermalCondR * dt);
const double alpha = compute_coupling_parameter(thermalCondR, edgeLen, chi);
// assemble the nodal quantities; group NOC on reference temp
// if NOC is < 0; Too will be greater than Tphyscial
// if NOC is > 0; Too will be less than Tphysical
// grouping NOC on H reverses the above, however, who knows which is best..
*assembledWallArea += aMag;
*referenceTemperature += thermalCondR*tempL*asq*inv_axdx - nonOrth;
*heatTransferCoefficient += -thermalCondR*tempR*asq*inv_axdx;
*normalHeatFlux += thermalCondR*(tempL-tempR)*asq*inv_axdx - nonOrth;
*robinCouplingParameter += alpha*aMag;
}
}
}
}
