//--------------------------------------------------------------------------
//-------- 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__);

    }
  }
}
//--------------------------------------------------------------------------
//-------- 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__);

    }
  }
}
//--------------------------------------------------------------------------
//-------- 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
AssembleRadTransElemSolverAlgorithm::execute()
{
  stk::mesh::MetaData & meta_data = realm_.meta_data();

  const int nDim = meta_data.spatial_dimension();

  // use edge-based length scale
  const bool useEdgeH = true;

  // extract current ordinate direction
  std::vector<double> Sk(nDim,0.0);
  radEqSystem_->get_current_ordinate(&Sk[0]);
  const double *p_Sk = &Sk[0];
  intensity_ = radEqSystem_->get_intensity();
  
  const double invPi = 1.0/(std::acos(-1.0));

   // space for LHS/RHS; nodesPerElem*nodesPerElem and nodesPerElem
  std::vector<double> lhs;
  std::vector<double> rhs;
  std::vector<stk::mesh::Entity> connected_nodes;

  // nodal fields to gather
  std::vector<double> ws_coordinates;
  std::vector<double> ws_intensity;
  std::vector<double> ws_absorption;
  std::vector<double> ws_scattering;
  std::vector<double> ws_scalarFlux;
  std::vector<double> ws_radiationSource;
  std::vector<double> ws_dualVolume;

  // 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;

  // 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 size_t 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_coordinates.resize(nodesPerElement*nDim);
    ws_intensity.resize(nodesPerElement);
    ws_absorption.resize(nodesPerElement);
    ws_scattering.resize(nodesPerElement);
    ws_scalarFlux.resize(nodesPerElement);
    ws_radiationSource.resize(nodesPerElement);
    ws_dualVolume.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);

     // pointers
    double *p_lhs = &lhs[0];
    double *p_rhs = &rhs[0];
    double *p_coordinates = &ws_coordinates[0];
    double *p_intensity = &ws_intensity[0];
    double *p_absorption = &ws_absorption[0];
    double *p_scattering = &ws_scattering[0];
    double *p_scalarFlux = &ws_scalarFlux[0];
    double *p_radiationSource = &ws_radiationSource[0];
    double *p_dualVolume = &ws_dualVolume[0];
    double *p_scs_areav = &ws_scs_areav[0];
    double *p_dndx = &ws_dndx[0];
    double *p_shape_function = &ws_shape_function[0];

    meSCS->shape_fcn(&p_shape_function[0]);

    for ( size_t 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 elem and its node relations
      unsigned elem_offset = k;

      //===============================================
      // gather nodal data; this is how we do it now..
      //===============================================
      stk::mesh::Entity const *  node_rels = b.begin_nodes(elem_offset);
      int num_nodes = b.num_nodes(elem_offset);

      // 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 * coords = stk::mesh::field_data(*coordinates_, node);

        // gather scalars
        p_intensity[ni]   = *stk::mesh::field_data(*intensity_, node);
        p_absorption[ni]  = *stk::mesh::field_data(*absorption_, node );
        p_scattering[ni]  = *stk::mesh::field_data(*scattering_, node );
        p_scalarFlux[ni]  = *stk::mesh::field_data(*scalarFlux_, node );
        p_radiationSource[ni] = *stk::mesh::field_data(*radiationSource_, node );
        p_dualVolume[ni]  = *stk::mesh::field_data(*dualNodalVolume_, node );

        // gather vectors
        const int offSet = ni*nDim;
        for ( int j=0; j < nDim; ++j ) {
          p_coordinates[offSet+j] = coords[j];
        }
      }

      // 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);

      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;

        // form sj*njdS (part of the lhs for central term; I*sj*njdS)
        double sjaj = 0.0;
        double asq = 0.0;
        for ( int j = 0; j < nDim; ++j ) {
          const double aj = p_scs_areav[ip*nDim+j];
          sjaj += p_Sk[j]*aj;
          asq += aj*aj;
        }
        const double aMag = std::sqrt(asq);

        // integration point interpolation
        double Iscs = 0.0;
        double extCoeffscs = 0.0;
        double ePscs = 0.0;
        double isotropicScatterscs = 0.0;
        double dualNodalVscs = 0.0;
        const int offSet = ip*nodesPerElement;
        for ( int ic = 0; ic < nodesPerElement; ++ic ) {
          const double r = p_shape_function[offSet+ic];
          
          // save of some variables
          const double I = p_intensity[ic];
          const double mua = p_absorption[ic];
          const double mus = p_scattering[ic];

          // interpolation to scs
          Iscs += r*I;
          extCoeffscs += r*(mua+mus);
          ePscs += r*p_radiationSource[ic];
          isotropicScatterscs += r*mus*p_scalarFlux[ic]/4.0*invPi;
          dualNodalVscs += r*p_dualVolume[ic];

          // assemble I*sj*njdS to lhs; left/right
          p_lhs[rowL+ic] += sjaj*r;
          p_lhs[rowR+ic] -= sjaj*r;
        }

        // rhs residual for I*sj*njdS
        p_rhs[il] -= Iscs*sjaj;
        p_rhs[ir] += Iscs*sjaj;

        // now work on SUCV stabilization terms; needed tau, hence second ic loop
        double h_edge = 0.0;
        for ( int j = 0; j < nDim; ++j ) {
          const double nj = p_scs_areav[ip*nDim+j]/aMag;
          const double dxj = p_coordinates[ir*nDim+j]-p_coordinates[il*nDim+j];
          h_edge += nj*dxj;
        }

        // alternative h
        const double h_vol = std::pow(dualNodalVscs, 1.0/(double)nDim);

        // form tau
        const double h = (useEdgeH) ? h_edge : h_vol;
        const double tau = std::sqrt(1.0/((2.0/h)*(2.0/h) + extCoeffscs*extCoeffscs));
	
        double sidIdxi = 0.0;
        for ( int ic = 0; ic < nodesPerElement; ++ic ) {
          const double r = p_shape_function[offSet+ic];

          // save of some variables
          const double I = p_intensity[ic];
          
          // SUCV -tau*sj*aj*(mua+mus)*I term; left/right (residual below)
          p_lhs[rowL+ic] += -tau*sjaj*r*extCoeffscs;
          p_lhs[rowR+ic] -= -tau*sjaj*r*extCoeffscs;
	  
          // SUCV diffusion-like term; -tau*si*dI/dxi*sjaj (residual below)
          double lhsfac = 0.0;
          const int offSetDnDx = nDim*nodesPerElement*ip + ic*nDim;
          for ( int j = 0; j < nDim; ++j ) {
            const double sjdNj = p_Sk[j]*p_dndx[offSetDnDx+j];
            sidIdxi += sjdNj*I;
            lhsfac += -sjdNj;
          }
          p_lhs[rowL+ic] += tau*sjaj*lhsfac;
          p_lhs[rowR+ic] -= tau*sjaj*lhsfac;
	  
        }
	
        // full sucv residual
	const double residual = -tau*sjaj*(sidIdxi + extCoeffscs*Iscs - ePscs - isotropicScatterscs);
	
        // residual; left and right
        p_rhs[il] -= residual;
        p_rhs[ir] += residual;
	
      }

      apply_coeff(connected_nodes, rhs, lhs, __FILE__);
    }

  }
}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleCourantReynoldsElemAlgorithm::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_.timeIntegrator_->get_time_step();
  const double small = 1.0e-16;

  // nodal fields to gather; gather everything other than what we are assembling
  std::vector<double> ws_vrtm;
  std::vector<double> ws_coordinates;
  std::vector<double> ws_density;
  std::vector<double> ws_viscosity;

  // deal with state
  ScalarFieldType &densityNp1 = density_->field_of_state(stk::mesh::StateNP1);

  // set courant/reynolds number to something small
  double maxCR[2] = {-1.0, -1.0};

  // 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();

    // algorithm related
    ws_vrtm.resize(nodesPerElement*nDim);
    ws_coordinates.resize(nodesPerElement*nDim);
    ws_density.resize(nodesPerElement);
    ws_viscosity.resize(nodesPerElement);

    // pointers.
    double *p_vrtm = &ws_vrtm[0];
    double *p_coordinates = &ws_coordinates[0];
    double *p_density = &ws_density[0];
    double *p_viscosity = &ws_viscosity[0];

    for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {

      // get elem
      stk::mesh::Entity elem = b[k];

      //===============================================
      // 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];

        // pointers to real data
        double * coords = stk::mesh::field_data(*coordinates_, node );
        double * vrtm = stk::mesh::field_data(*velocityRTM_, node );

        // gather scalars
        p_density[ni]   = *stk::mesh::field_data(densityNp1, node);
        p_viscosity[ni] = *stk::mesh::field_data(*viscosity_, node);

        // gather vectors
        const int offSet = ni*nDim;
        for ( int j = 0; j < nDim; ++j ) {
          p_coordinates[offSet+j] = coords[j];
          p_vrtm[offSet+j] = vrtm[j];
        }
      }

      // compute cfl and Re along each edge
      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];

        double udotx = 0.0;
        double dxSq = 0.0;
        for ( int j = 0; j < nDim; ++j ) {
          double ujIp = 0.5*(p_vrtm[il*nDim+j]+p_vrtm[il*nDim+j]);
          double dxj = p_coordinates[ir*nDim+j] - p_coordinates[il*nDim+j];
          udotx += dxj*ujIp;
          dxSq += dxj*dxj;
        }

        udotx = std::abs(udotx);
        maxCR[0] = std::max(maxCR[0], std::abs(udotx*dt/dxSq));

        double diffIp = 0.5*( p_viscosity[il]/p_density[il] + p_viscosity[ir]/p_density[ir] );
        maxCR[1] = std::max(maxCR[1], udotx/(diffIp+small));
      }
    }
  }

  // parallel max
  double g_maxCR[2]  = {};
  stk::ParallelMachine comm = NaluEnv::self().parallel_comm();
  stk::all_reduce_max(comm, maxCR, g_maxCR, 2);

  // sent to realm
  realm_.maxCourant_ = g_maxCR[0];
  realm_.maxReynolds_ = g_maxCR[1];

}
//--------------------------------------------------------------------------
//-------- execute ---------------------------------------------------------
//--------------------------------------------------------------------------
void
AssembleNodalGradUElemAlgorithm::execute()
{

  stk::mesh::MetaData & meta_data = realm_.meta_data();

  const int nDim = meta_data.spatial_dimension();

  // extract fields
  ScalarFieldType *dualNodalVolume = meta_data.get_field<ScalarFieldType>(stk::topology::NODE_RANK, "dual_nodal_volume");
  VectorFieldType *coordinates = meta_data.get_field<VectorFieldType>(stk::topology::NODE_RANK, realm_.get_coordinates_name());

  // nodal fields to gather; gather everything other than what we are assembling
  std::vector<double> ws_vectorQ;
  std::vector<double> ws_dualVolume;
  std::vector<double> ws_coordinates;

  // geometry related to populate
  std::vector<double> ws_scs_areav;
  std::vector<double> ws_shape_function;

  // ip data
  std::vector<double>qIp(nDim);

  // 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();

    // algorithm related
    ws_vectorQ.resize(nodesPerElement*nDim);
    ws_dualVolume.resize(nodesPerElement);
    ws_coordinates.resize(nodesPerElement*nDim);
    ws_scs_areav.resize(numScsIp*nDim);
    ws_shape_function.resize(numScsIp*nodesPerElement);

    // pointers.
    double *p_vectorQ = &ws_vectorQ[0];
    double *p_dualVolume = &ws_dualVolume[0];
    double *p_coordinates = &ws_coordinates[0];
    double *p_scs_areav = &ws_scs_areav[0];
    double *p_shape_function = &ws_shape_function[0];

    if ( useShifted_ )
      meSCS->shifted_shape_fcn(&p_shape_function[0]);
    else
      meSCS->shape_fcn(&p_shape_function[0]);

    for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {

      //===============================================
      // 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 );

      // note: we absolutely need to gather coords since it
      // is required to compute the area vector. however,
      // ws_scalarQ and ws_dualVolume are choices to avoid
      // field data call for interpolation

      for ( int ni = 0; ni < num_nodes; ++ni ) {
        stk::mesh::Entity node = node_rels[ni];

        // pointers to real data
        double * coords = stk::mesh::field_data(*coordinates, node);
        double * vectorQ = stk::mesh::field_data(*vectorQ_, node);

        // gather scalars
        p_dualVolume[ni] = *stk::mesh::field_data(*dualNodalVolume, node);

        // gather vectors
        const int offSet = ni*nDim;
        for ( int j=0; j < nDim; ++j ) {
          p_coordinates[offSet+j] = coords[j];
          p_vectorQ[offSet+j] = vectorQ[j];
        }
      }

      // compute geometry
      double scs_error = 0.0;
      meSCS->determinant(1, &p_coordinates[0], &p_scs_areav[0], &scs_error);

      // start assembly
      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];

        stk::mesh::Entity nodeL = node_rels[il];
        stk::mesh::Entity nodeR = node_rels[ir];

        // pointer to fields to assemble
        double *gradQL = stk::mesh::field_data(*dqdx_, nodeL);
        double *gradQR = stk::mesh::field_data(*dqdx_, nodeR);

        // interpolate to scs point; operate on saved off ws_field
        for (int j=0; j < nDim; ++j )
          qIp[j] = 0.0;

        const int offSet = ip*nodesPerElement;
        for ( int ic = 0; ic < nodesPerElement; ++ic ) {
          const double r = p_shape_function[offSet+ic];
          for ( int j = 0; j < nDim; ++j ) {
            qIp[j] += r*p_vectorQ[ic*nDim+j];
          }
        }

        // left and right volume
        double inv_volL = 1.0/p_dualVolume[il];
        double inv_volR = 1.0/p_dualVolume[ir];

        // assemble to il/ir
        for ( int i = 0; i < nDim; ++i ) {
          const int row_gradQ = i*nDim;
          const double qip = qIp[i];
          for ( int j = 0; j < nDim; ++j ) {
            double fac = qip*p_scs_areav[ip*nDim+j];
            gradQL[row_gradQ+j] += fac*inv_volL;
            gradQR[row_gradQ+j] -= fac*inv_volR;
          }
        }
      }
    }
  }
}
Exemplo n.º 7
0
//--------------------------------------------------------------------------
//-------- assemble_edge_mdot ----------------------------------------------
//--------------------------------------------------------------------------
void
ComputeMdotElemAlgorithm::assemble_edge_mdot()
{

  stk::mesh::BulkData & bulk_data = realm_.bulk_data();
  stk::mesh::MetaData & meta_data = realm_.meta_data();

  // zero out edge mdot
  stk::mesh::Selector s_all_edges
    = (meta_data.locally_owned_part() | meta_data.globally_shared_part())
    &stk::mesh::selectUnion(partVec_);
  stk::mesh::BucketVector const& edge_buckets =
    realm_.get_buckets( stk::topology::EDGE_RANK, s_all_edges );
  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();
    double * edgeMdot = stk::mesh::field_data(*edgeMassFlowRate_, b);
    for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {
        edgeMdot[k] = 0.0;
    }
  }

  // now assemble by looping over elements; looks like the edge-assembled area
  // setup for buckets; union parts and ask for locally owned
  stk::mesh::Selector s_locally_owned_union = meta_data.locally_owned_part()
      &stk::mesh::selectUnion(partVec_);
  stk::mesh::BucketVector const& element_buckets =
    realm_.get_buckets( stk::topology::ELEMENT_RANK, s_locally_owned_union );

  for ( stk::mesh::BucketVector::const_iterator ib = element_buckets.begin();
        ib != element_buckets.end() ; ++ib ) {
    stk::mesh::Bucket & b = **ib ;

    // extract master element
    MasterElement *meSCS = realm_.get_surface_master_element(b.topology());

    // extract master element specifics
    const int *lrscv = meSCS->adjacentNodes();

    const stk::mesh::Bucket::size_type length   = b.size();

    for ( stk::mesh::Bucket::size_type k = 0 ; k < length ; ++k ) {

      // extract element
      stk::mesh::Entity elem = b[k];

      // ip data for this element; scs mdot
      const double *scsMdot = stk::mesh::field_data(*massFlowRate_, elem );

      // Use node Entity because we'll need to call BulkData::identifier(.).
      stk::mesh::Entity const * elem_node_rels = b.begin_nodes(k);

      // iterate edges
      stk::mesh::Entity const * elem_edge_rels = b.begin_edges(k);
      int num_edges = b.num_edges(k);

      for ( int nedge = 0; nedge < num_edges; ++nedge ) {

        // get edge and area_vector
        stk::mesh::Entity edge = elem_edge_rels[nedge];
        double * edgeMdot = stk::mesh::field_data(*edgeMassFlowRate_, edge );

        // extract edge->node relations
        stk::mesh::Entity const * edge_node_rels = bulk_data.begin_nodes(edge);
        ThrowAssert( 2 == bulk_data.num_nodes(edge) );

        // work towards "sign" convention

        // extract a local node; choose to pick L and follow it through
        const int iloc_L = lrscv[2*nedge];

        // get global identifiers for nodes Left and Right from the element
        const size_t iglob_Lelem = bulk_data.identifier(elem_node_rels[iloc_L]);
        const size_t iglob_Ledge = bulk_data.identifier(edge_node_rels[0]);

        // determine the sign value for area vector; if Left node is the same,
        // then the element and edge relations are aligned
        const double sign = ( iglob_Lelem == iglob_Ledge ) ? 1.0 : -1.0;
        *edgeMdot += scsMdot[nedge]*sign;
      }
    }
  }

  // parallel reduce
  std::vector<stk::mesh::FieldBase*> sum_fields(1, edgeMassFlowRate_);
  stk::mesh::parallel_sum(bulk_data, sum_fields);

}