//--------------------------------------------------------------------------
//-------- 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
AssembleScalarEdgeSolverAlgorithm::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; always edge connectivity
const int nodesPerEdge = 2;
const int lhsSize = nodesPerEdge*nodesPerEdge;
const int rhsSize = 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];
// deal with state
ScalarFieldType &scalarQNp1 = scalarQ_->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;
}
// get edge
stk::mesh::Entity edge = b[k];
stk::mesh::Entity const * edge_node_rels = bulk_data.begin_nodes(edge);
// sanity check on number or nodes
ThrowAssert( bulk_data.num_nodes(edge) == 2 );
// pointer to edge area vector
for ( int j = 0; j < nDim; ++j )
p_areaVec[j] = av[k*nDim+j];
const double tmdot = mdot[k];
// 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 * dqdxL = stk::mesh::field_data(*dqdx_, nodeL);
const double * dqdxR = stk::mesh::field_data(*dqdx_, nodeR);
const double * vrtmL = stk::mesh::field_data(*velocityRTM_, nodeL);
const double * vrtmR = stk::mesh::field_data(*velocityRTM_, nodeR);
const double qNp1L = *stk::mesh::field_data(scalarQNp1, nodeL);
const double qNp1R = *stk::mesh::field_data(scalarQNp1, nodeR);
const double densityL = *stk::mesh::field_data(densityNp1, nodeL);
const double densityR = *stk::mesh::field_data(densityNp1, nodeR);
const double diffFluxCoeffL = *stk::mesh::field_data(*diffFluxCoeff_, nodeL);
const double diffFluxCoeffR = *stk::mesh::field_data(*diffFluxCoeff_, nodeR);
// 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];
asq += axj*axj;
axdx += axj*dxj;
udotx += 0.5*dxj*(vrtmL[j] + vrtmR[j]);
}
const double inv_axdx = 1.0/axdx;
// ip props
const double viscIp = 0.5*(diffFluxCoeffL + diffFluxCoeffR);
const double diffIp = 0.5*(diffFluxCoeffL/densityL + diffFluxCoeffR/densityR);
// Peclet factor
double pecfac = hybridFactor*udotx/(diffIp+small);
pecfac = pecfac*pecfac/(5.0 + pecfac*pecfac);
const double om_pecfac = 1.0-pecfac;
// left and right extrapolation; add in diffusion calc
double dqL = 0.0;
double dqR = 0.0;
double nonOrth = 0.0;
for ( int j = 0; j < nDim; ++j ) {
const double dxj = coordR[j] - coordL[j];
dqL += 0.5*dxj*dqdxL[j];
dqR += 0.5*dxj*dqdxR[j];
// now non-orth (over-relaxed procedure of Jasek)
const double axj = p_areaVec[j];
const double kxj = axj - asq*inv_axdx*dxj;
const double GjIp = 0.5*(dqdxL[j] + dqdxR[j]);
nonOrth += -viscIp*kxj*GjIp;
}
// add limiter if appropriate
double limitL = 1.0;
double limitR = 1.0;
const double dq = qNp1R - qNp1L;
if ( useLimiter ) {
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
const double qIpL = qNp1L + dqL*hoUpwind*limitL;
const double qIpR = qNp1R - dqR*hoUpwind*limitR;
//====================================
// diffusive flux
//====================================
double lhsfac = -viscIp*asq*inv_axdx;
double diffFlux = lhsfac*(qNp1R - qNp1L) + nonOrth;
// first left
p_lhs[0] = -lhsfac;
p_lhs[1] = +lhsfac;
p_rhs[0] = -diffFlux;
// now right
p_lhs[2] = +lhsfac;
p_lhs[3] = -lhsfac;
p_rhs[1] = diffFlux;
//====================================
// advective flux
//====================================
// 2nd order central
const double qIp = 0.5*( qNp1L + qNp1R );
// 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);
// upwind advection (includes 4th); left node
double alhsfac = 0.5*(tmdot+std::abs(tmdot))*pecfac*alphaUpw
+ 0.5*alpha*om_pecfac*tmdot;
p_lhs[0] += alhsfac;
p_lhs[2] -= alhsfac;
// upwind advection; right node
alhsfac = 0.5*(tmdot-std::abs(tmdot))*pecfac*alphaUpw
+ 0.5*alpha*om_pecfac*tmdot;
p_lhs[3] -= alhsfac;
p_lhs[1] += alhsfac;
// central; left; collect terms on alpha and alphaUpw
alhsfac = 0.5*tmdot*(pecfac*om_alphaUpw + om_pecfac*om_alpha);
p_lhs[0] += alhsfac;
p_lhs[1] += alhsfac;
// central; right; collect terms on alpha and alphaUpw
p_lhs[2] -= alhsfac;
p_lhs[3] -= alhsfac;
// total flux left
p_rhs[0] -= aflux;
// total flux right
p_rhs[1] += aflux;
apply_coeff(connected_nodes, 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
AssembleMomentumEdgeContactSolverAlgorithm::execute()
{
stk::mesh::MetaData & meta_data = realm_.meta_data();
stk::mesh::BulkData & bulk_data = realm_.bulk_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; (nodesPerElem+1)*nDim*(nodesPerElem+1)*nDim; (nodesPerElem+1)*nDim
std::vector<double> lhs;
std::vector<double> rhs;
std::vector<stk::mesh::Entity> connected_nodes;
// space for dui/dxj. This variable is the modifed 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];
// space for interpolated right state (halo)
double densityR;
double viscosityR;
std::vector<double> uNp1R(nDim);
std::vector<double> dudxR(nDim*nDim);
// interpolate nodal values to point-in-elem
const int sizeOfScalarField = 1;
const int sizeOfVectorField = nDim;
const int sizeOfTensorField = nDim*nDim;
// deal with state
VectorFieldType &velocityNp1 = velocity_->field_of_state(stk::mesh::StateNP1);
ScalarFieldType &densityNp1 = density_->field_of_state(stk::mesh::StateNP1);
// mesh motion
std::vector<double> vrtmL(nDim);
std::vector<double> vrtmR(nDim);
double * p_vrtmL = &vrtmL[0];
double * p_vrtmR = &vrtmR[0];
// parallel communicate ghosted entities
if ( NULL != realm_.contactManager_->contactGhosting_ )
stk::mesh::communicate_field_data(*(realm_.contactManager_->contactGhosting_), ghostFieldVec_);
// iterate contactInfoVec_
std::vector<ContactInfo *>::iterator ii;
for( ii=realm_.contactManager_->contactInfoVec_.begin();
ii!=realm_.contactManager_->contactInfoVec_.end(); ++ii ) {
// get master element type for this contactInfo
MasterElement *meSCS = (*ii)->meSCS_;
const int nodesPerElement = meSCS->nodesPerElement_;
std::vector<double> elemNodalP(nodesPerElement);
std::vector<double> elemNodalUnp1(nDim*nodesPerElement);
std::vector<double> elemNodalVisc(nodesPerElement);
std::vector<double> elemNodalRho(nodesPerElement);
std::vector<double> elemNodalDudx(nDim*nDim*nodesPerElement);
std::vector<double> shpfc(nodesPerElement);
// resize some things; matrix related
const int npePlusOne = nodesPerElement+1;
const int lhsSize = npePlusOne*nDim*npePlusOne*nDim;
const int rhsSize = npePlusOne*nDim;
lhs.resize(lhsSize);
rhs.resize(rhsSize);
connected_nodes.resize(npePlusOne);
// pointer to lhs/rhs
double *p_lhs = &lhs[0];
double *p_rhs = &rhs[0];
// scaling for lhs
const double inv_nodesPerElement = 1.0/double(nodesPerElement);
// iterate halo face nodes
std::map<uint64_t, HaloInfo *>::iterator iterHalo;
for (iterHalo = (*ii)->haloInfoMap_.begin();
iterHalo != (*ii)->haloInfoMap_.end();
++iterHalo) {
// halo info object of interest
HaloInfo * infoObject = (*iterHalo).second;
// zeroing of lhs/rhs
for ( int k = 0; k < lhsSize; ++k ) {
p_lhs[k] = 0.0;
}
for ( int k = 0; k < rhsSize; ++k ) {
p_rhs[k] = 0.0;
}
// pointer to edge area vector and mdot
const double *p_areaVec = &infoObject->haloEdgeAreaVec_[0];
const double tmdot = *stk::mesh::field_data(*haloMdot_, infoObject->faceNode_);
// extract element mesh object and global id for face node
stk::mesh::Entity elem = infoObject->owningElement_;
stk::mesh::Entity const* elem_node_rels = bulk_data.begin_nodes(elem);
const int num_nodes = bulk_data.num_nodes(elem);
// now load the elemental values for future interpolation; fill in connected nodes
connected_nodes[0] = infoObject->faceNode_;
for ( int ni = 0; ni < num_nodes; ++ni ) {
stk::mesh::Entity node = elem_node_rels[ni];
connected_nodes[ni+1] = node;
elemNodalRho[ni] = *stk::mesh::field_data(densityNp1, node);
elemNodalVisc[ni] = *stk::mesh::field_data(*viscosity_, node);
// load up vectors/tensor
const double *uNp1 = stk::mesh::field_data(velocityNp1, node );
const double *dudx = stk::mesh::field_data(*dudx_, node );
for ( int i = 0; i < nDim; ++i ) {
const int offSet = i*nodesPerElement + ni;
elemNodalUnp1[offSet] = uNp1[i];
const int rowI = i*nDim;
const int offSetT = i*nodesPerElement*nDim;
for ( int j = 0; j < nDim; ++j ) {
elemNodalDudx[offSetT+j*nodesPerElement+ni] = dudx[rowI+j];
}
}
}
// extract nodal fields; right state is Halo and requires inperpolation
const double *coordL = stk::mesh::field_data(*coordinates_, infoObject->faceNode_);
const double *coordR = &infoObject->haloNodalCoords_[0];
const double *dudxL = stk::mesh::field_data(*dudx_, infoObject->faceNode_);
meSCS->interpolatePoint(
sizeOfTensorField,
&(infoObject->isoParCoords_[0]),
&elemNodalDudx[0],
&(dudxR[0]));
const double *uNp1L = stk::mesh::field_data(velocityNp1, infoObject->faceNode_);
meSCS->interpolatePoint(
sizeOfVectorField,
&(infoObject->isoParCoords_[0]),
&elemNodalUnp1[0],
&(uNp1R[0]));
const double densityL = *stk::mesh::field_data(densityNp1, infoObject->faceNode_);
meSCS->interpolatePoint(
sizeOfScalarField,
&(infoObject->isoParCoords_[0]),
&elemNodalRho[0],
&densityR);
const double viscosityL = *stk::mesh::field_data(*viscosity_, infoObject->faceNode_);
meSCS->interpolatePoint(
sizeOfScalarField,
&(infoObject->isoParCoords_[0]),
&elemNodalVisc[0],
&viscosityR);
// copy to velocity relative to mesh; squeeze in extrapolated values
for ( int i = 0; i < nDim; ++i ) {
p_vrtmL[i] = uNp1L[i];
p_vrtmR[i] = uNp1R[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];
}
}
// deal with mesh motion
if ( meshMotion_ ) {
const double * meshVelocityL = stk::mesh::field_data(*meshVelocity_, infoObject->faceNode_);
const double * meshVelocityR = &(infoObject->haloMeshVelocity_[0]);
for (int j = 0; j < nDim; ++j ) {
p_vrtmL[j] -= meshVelocityL[j];
p_vrtmR[j] -= meshVelocityR[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*(p_vrtmL[j] + p_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;
}
}
// divU
double divU = 0.0;
for ( int j = 0; j < nDim; ++j)
divU += p_duidxj[j*nDim+j];
// 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);
// 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
meSCS->general_shape_fcn(1, &(infoObject->isoParCoords_[0]), &shpfc[0]);
const double tflux = aflux + dflux;
const int indexL = i;
// setup for LHS; row left is easy
const int rowL = indexL * npePlusOne * nDim;
const int rLiL = rowL+indexL;
// total flux left
p_rhs[indexL] -= tflux;
// for ease of reading, scale left node by nodesPerElement
for ( int ni = 0; ni < num_nodes; ++ni ) {
const int indexR = i + nDim*(ni+1);
const int rLiR = rowL+indexR;
//==============================
// advection first
//==============================
// 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*inv_nodesPerElement;
// upwind advection (incldues 4th); right node
alhsfac = 0.5*(tmdot-std::abs(tmdot))*pecfac*alphaUpw
+ 0.5*alpha*om_pecfac*tmdot;
p_lhs[rLiR] += alhsfac*shpfc[ni];
// central; left; collect terms on alpha and alphaUpw
alhsfac = 0.5*tmdot*(pecfac*om_alphaUpw + om_pecfac*om_alpha);
p_lhs[rLiL] += alhsfac*inv_nodesPerElement;
p_lhs[rLiR] += alhsfac*shpfc[ni];
// central; right n/a
//==============================
// diffusion second
//==============================
const double axi = p_areaVec[i];
//diffusion; row IL
p_lhs[rLiL] -= dlhsfac*inv_nodesPerElement;
p_lhs[rLiR] += dlhsfac*shpfc[ni];
// diffusion; row IR; n/a
// 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*(ni+1);
// first left; IL,IL; IL,IR
p_lhs[rowL + colL] -= lhsfacNS*inv_nodesPerElement;
p_lhs[rowL + colR] += lhsfacNS*shpfc[ni];
// now right, IR,IL; IR,IR; n/a
}
}
}
// apply to linear system
apply_coeff(connected_nodes, rhs, lhs, __FILE__);
}
}
}
