ERF_SlowRhsPost.cpp File Reference

#include <AMReX.H>
#include <ERF_SrcHeaders.H>
#include <ERF_TI_slow_headers.H>
#include <ERF_EBAdvection.H>
#include <ERF_EBRedistribute.H>

Include dependency graph for ERF_SlowRhsPost.cpp:

Functions
void	erf_slow_rhs_post (int level, int finest_level, int nrk, Real dt, int n_qstate, Vector< MultiFab > &S_rhs, Vector< MultiFab > &S_old, Vector< MultiFab > &S_new, Vector< MultiFab > &S_data, const MultiFab &S_prim, MultiFab &avg_xmom, MultiFab &avg_ymom, MultiFab &avg_zmom, const MultiFab &xvel, const MultiFab &yvel, const MultiFab &, const MultiFab &source, const MultiFab *SmnSmn, const MultiFab *eddyDiffs, MultiFab *Hfx1, MultiFab *Hfx2, MultiFab *Hfx3, MultiFab *Q1fx1, MultiFab *Q1fx2, MultiFab *Q1fx3, MultiFab *Q2fx3, MultiFab *Diss, const Geometry geom, const SolverChoice &solverChoice, std::unique_ptr< SurfaceLayer > &SurfLayer, const Gpu::DeviceVector< BCRec > &domain_bcs_type_d, const Vector< BCRec > &domain_bcs_type_h, std::unique_ptr< MultiFab > &z_phys_nd, std::unique_ptr< MultiFab > &z_phys_cc, std::unique_ptr< MultiFab > &ax, std::unique_ptr< MultiFab > &ay, std::unique_ptr< MultiFab > &az, std::unique_ptr< MultiFab > &detJ, MultiFab *detJ_new, Gpu::DeviceVector< Real > &stretched_dz_d, Vector< std::unique_ptr< MultiFab >> &mapfac, amrex::EBFArrayBoxFactory const &ebfact, YAFluxRegister *fr_as_crse, YAFluxRegister *fr_as_fine, std::unique_ptr< ReadBndryPlanes > &m_r2d)

Function Documentation

erf_slow_rhs_post()

void erf_slow_rhs_post	(	int	level,
		int	finest_level,
		int	nrk,
		Real	dt,
		int	n_qstate,
		Vector< MultiFab > &	S_rhs,
		Vector< MultiFab > &	S_old,
		Vector< MultiFab > &	S_new,
		Vector< MultiFab > &	S_data,
		const MultiFab &	S_prim,
		MultiFab &	avg_xmom,
		MultiFab &	avg_ymom,
		MultiFab &	avg_zmom,
		const MultiFab &	xvel,
		const MultiFab &	yvel,
		const MultiFab &	,
		const MultiFab &	source,
		const MultiFab *	SmnSmn,
		const MultiFab *	eddyDiffs,
		MultiFab *	Hfx1,
		MultiFab *	Hfx2,
		MultiFab *	Hfx3,
		MultiFab *	Q1fx1,
		MultiFab *	Q1fx2,
		MultiFab *	Q1fx3,
		MultiFab *	Q2fx3,
		MultiFab *	Diss,
		const Geometry	geom,
		const SolverChoice &	solverChoice,
		std::unique_ptr< SurfaceLayer > &	SurfLayer,
		const Gpu::DeviceVector< BCRec > &	domain_bcs_type_d,
		const Vector< BCRec > &	domain_bcs_type_h,
		std::unique_ptr< MultiFab > &	z_phys_nd,
		std::unique_ptr< MultiFab > &	z_phys_cc,
		std::unique_ptr< MultiFab > &	ax,
		std::unique_ptr< MultiFab > &	ay,
		std::unique_ptr< MultiFab > &	az,
		std::unique_ptr< MultiFab > &	detJ,
		MultiFab *	detJ_new,
		Gpu::DeviceVector< Real > &	stretched_dz_d,
		Vector< std::unique_ptr< MultiFab >> &	mapfac,
		amrex::EBFArrayBoxFactory const &	ebfact,
		YAFluxRegister *	fr_as_crse,
		YAFluxRegister *	fr_as_fine,
		std::unique_ptr< ReadBndryPlanes > &	m_r2d
	)

Function for computing the slow RHS for the evolution equations for the scalars other than density or potential temperature

Parameters

[in]	evel	level of resolution
[in]	finest_level	finest level of resolution
[in]	nrk	which RK stage
[in]	dt	slow time step
[out]	S_rhs	RHS computed here
[in]	S_old	solution at start of time step
[in]	S_new	solution at end of current RK stage
[in]	S_data	current solution
[in]	S_prim	primitive variables (i.e. conserved variables divided by density)
[in]	avg_xmom
[in]	avg_ymom
[in]	avg_zmom
[in]	xvel	x-component of velocity
[in]	yvel	y-component of velocity
[in]	zvel	z-component of velocity
[in]	source	source terms for conserved variables
[in]	SmnSmn	strain rate magnitude
[in]	eddyDiffs	diffusion coefficients for LES turbulence models
[in]	Hfx3	heat flux in z-dir
[in]	Diss	dissipation of turbulent kinetic energy
[in]	geom	Container for geometric information
[in]	solverChoice	Container for solver parameters
[in]	SurfLayer	Pointer to SurfaceLayer class for Monin-Obukhov Similarity Theory boundary condition
[in]	domain_bcs_type_d	device vector for domain boundary conditions
[in]	z_phys_nd	height coordinate at nodes
[in]	ax	area fractions on x-faces
[in]	ay	area fractions on y-faces
[in]	az	area fractions on z-faces
[in]	detJ	Jacobian of the metric transformation at start of time step (= 1 if use_terrain is false)
[in]	detJ_new	Jacobian of the metric transformation at new RK stage time (= 1 if use_terrain is false)
[in]	mapfac	map factors
[in,out]	fr_as_crse	YAFluxRegister at level l at level l / l+1 interface
[in,out]	fr_as_fine	YAFluxRegister at level l at level l-1 / l interface

{
    BL_PROFILE_REGION("erf_slow_rhs_post()");
 
    const BCRec* bc_ptr_d = domain_bcs_type_d.data();
    const BCRec* bc_ptr_h = domain_bcs_type_h.data();
 
    AdvChoice  ac = solverChoice.advChoice;
    DiffChoice dc = solverChoice.diffChoice;
    TurbChoice tc = solverChoice.turbChoice[level];
 
    const MultiFab*  t_mean_mf = nullptr;
    if (SurfLayer) { t_mean_mf = SurfLayer->get_mac_avg(level,2); }
 
    const bool l_use_terrain      = (solverChoice.mesh_type != MeshType::ConstantDz);
    const bool l_moving_terrain   = (solverChoice.terrain_type == TerrainType::MovingFittedMesh);
    const bool l_reflux = ( (solverChoice.coupling_type == CouplingType::TwoWay) && (nrk == 2) && (finest_level > 0) );
    if (l_moving_terrain) AMREX_ALWAYS_ASSERT(l_use_terrain);
 
    const bool l_anelastic   = solverChoice.anelastic[level];
 
    const bool l_use_KE         = ( tc.use_tke );
    const bool l_need_SmnSmn    = ( tc.les_type  == LESType::Deardorff ||
                                    tc.rans_type == RANSType::kEqn );
    const bool l_advect_KE      = ( tc.use_tke && tc.advect_tke );
    const bool l_use_diff       = ((dc.molec_diff_type != MolecDiffType::None) ||
                                   (tc.les_type        !=       LESType::None) ||
                                   (tc.rans_type       !=      RANSType::None) ||
                                   (tc.pbl_type        !=       PBLType::None) );
    const bool l_use_turb       = ( tc.les_type  == LESType::Smagorinsky ||
                                    tc.les_type  == LESType::Deardorff   ||
                                    tc.rans_type == RANSType::kEqn       ||
                                    tc.pbl_type  == PBLType::MYJ         ||
                                    tc.pbl_type  == PBLType::MYNN25      ||
                                    tc.pbl_type  == PBLType::MYNNEDMF    ||
                                    tc.pbl_type  == PBLType::YSU ||
                                    tc.pbl_type  == PBLType::MRF );
    const bool l_rotate         = (solverChoice.use_rotate_surface_flux);
    const bool l_do_scalar      = (solverChoice.transport_scalar);
    amrex::ignore_unused(m_r2d);
 
    const Box& domain = geom.Domain();
 
    const GpuArray<Real, AMREX_SPACEDIM> dxInv = geom.InvCellSizeArray();
    const Real* dx = geom.CellSize();
 
    // *************************************************************************
    // Set gravity as a vector
    // *************************************************************************
    const    Array<Real,AMREX_SPACEDIM> grav{zero, zero, -solverChoice.gravity};
    const GpuArray<Real,AMREX_SPACEDIM> grav_gpu{grav[0], grav[1], grav[2]};
 
    // *************************************************************************
    // Pre-computed quantities
    // *************************************************************************
    int nvars                     = S_data[IntVars::cons].nComp();
    const BoxArray& ba            = S_data[IntVars::cons].boxArray();
    const DistributionMapping& dm = S_data[IntVars::cons].DistributionMap();
 
    std::unique_ptr<MultiFab> dflux_x;
    std::unique_ptr<MultiFab> dflux_y;
    std::unique_ptr<MultiFab> dflux_z;
 
    if (l_use_diff) {
        IntVect ng(0,0,1);
        dflux_x = std::make_unique<MultiFab>(convert(ba,IntVect(1,0,0)), dm, 1, ng);
        dflux_y = std::make_unique<MultiFab>(convert(ba,IntVect(0,1,0)), dm, 1, ng);
        dflux_z = std::make_unique<MultiFab>(convert(ba,IntVect(0,0,1)), dm, 1, 0);
    } else {
        dflux_x = nullptr;
        dflux_y = nullptr;
        dflux_z = nullptr;
    }
 
    // Valid vars
    Vector<int> is_valid_slow_var; is_valid_slow_var.resize(RhoQ1_comp+1,0);
    if (l_use_KE)    { is_valid_slow_var[    RhoKE_comp] = 1; }
    if (l_do_scalar) { is_valid_slow_var[RhoScalar_comp] = 1; }
    if (solverChoice.moisture_type != MoistureType::None) {
         is_valid_slow_var[RhoQ1_comp] = 1;
    }
 
    // *************************************************************************
    // Calculate cell-centered eddy viscosity & diffusivities
    //
    // Notes -- we fill all the data in ghost cells before calling this so
    //    that we can fill the eddy viscosity in the ghost regions and
    //    not have to call a boundary filler on this data itself
    //
    // LES - updates both horizontal and vertical eddy viscosityS_tmp components
    // PBL - only updates vertical eddy viscosity components so horizontal
    //       components come from the LES model or are left as zero.
    // *************************************************************************
 
    // *************************************************************************
    // Define updates and fluxes in the current RK stage
    // *************************************************************************
#ifdef _OPENMP
#pragma omp parallel if (Gpu::notInLaunchRegion())
#endif
    {
      std::array<FArrayBox,AMREX_SPACEDIM> flux;
 
      int start_comp;
      int   num_comp;
 
      // Cell-centered masks for EB (used for flux interpolation)
      iMultiFab physbnd_mask;
      bool already_on_centroids = false;
      if (solverChoice.terrain_type == TerrainType::EB) {
          physbnd_mask.define(S_data[IntVars::cons].boxArray(), S_data[IntVars::cons].DistributionMap(), 1, 1);
          physbnd_mask.BuildMask(geom.Domain(), geom.periodicity(), 1, 1, 0, 1);
      }
 
      for (MFIter mfi(S_data[IntVars::cons],TilingIfNotGPU()); mfi.isValid(); ++mfi) {
 
        Box tbx  = mfi.tilebox();
 
        // *************************************************************************
        // Define flux arrays for use in advection
        // *************************************************************************
        for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) {
            if (solverChoice.terrain_type != TerrainType::EB) {
                flux[dir].resize(surroundingNodes(tbx,dir),nvars,The_Async_Arena());
            } else {
                flux[dir].resize(surroundingNodes(tbx,dir).grow(1),nvars,The_Async_Arena());
            }
            flux[dir].setVal<RunOn::Device>(0);
        }
        const GpuArray<const Array4<Real>, AMREX_SPACEDIM>
            flx_arr{{AMREX_D_DECL(flux[0].array(), flux[1].array(), flux[2].array())}};
 
        // *************************************************************************
        // Define Array4's
        // *************************************************************************
        const Array4<const Real> & old_cons   = S_old[IntVars::cons].array(mfi);
        const Array4<      Real> & cell_rhs   = S_rhs[IntVars::cons].array(mfi);
 
        const Array4<      Real> & new_cons  = S_new[IntVars::cons].array(mfi);
        const Array4<      Real> & new_xmom  = S_new[IntVars::xmom].array(mfi);
        const Array4<      Real> & new_ymom  = S_new[IntVars::ymom].array(mfi);
        const Array4<      Real> & new_zmom  = S_new[IntVars::zmom].array(mfi);
 
        const Array4<      Real> & cur_cons  = S_data[IntVars::cons].array(mfi);
        const Array4<const Real> & cur_prim  = S_prim.array(mfi);
        const Array4<      Real> & cur_xmom  = S_data[IntVars::xmom].array(mfi);
        const Array4<      Real> & cur_ymom  = S_data[IntVars::ymom].array(mfi);
        const Array4<      Real> & cur_zmom  = S_data[IntVars::zmom].array(mfi);
 
        Array4<Real> avg_xmom_arr = avg_xmom.array(mfi);
        Array4<Real> avg_ymom_arr = avg_ymom.array(mfi);
        Array4<Real> avg_zmom_arr = avg_zmom.array(mfi);
 
        const Array4<const Real> & u = xvel.array(mfi);
        const Array4<const Real> & v = yvel.array(mfi);
 
        const Array4<Real const>& mu_turb = l_use_turb ? eddyDiffs->const_array(mfi) : Array4<const Real>{};
 
        const Array4<const Real>& z_nd         = z_phys_nd->const_array(mfi);
        const Array4<const Real>& z_cc         = z_phys_cc->const_array(mfi);
        const Array4<const Real>& detJ_new_arr = l_moving_terrain ? detJ_new->const_array(mfi)    : Array4<const Real>{};
 
        // Map factors
        const Array4<const Real>& mf_mx = mapfac[MapFacType::m_x]->const_array(mfi);
        const Array4<const Real>& mf_ux = mapfac[MapFacType::u_x]->const_array(mfi);
        const Array4<const Real>& mf_vx = mapfac[MapFacType::v_x]->const_array(mfi);
        const Array4<const Real>& mf_my = mapfac[MapFacType::m_y]->const_array(mfi);
        const Array4<const Real>& mf_uy = mapfac[MapFacType::u_y]->const_array(mfi);
        const Array4<const Real>& mf_vy = mapfac[MapFacType::v_y]->const_array(mfi);
 
        // SmnSmn for KE src with Deardorff or k-eqn RANS
        const Array4<const Real>& SmnSmn_a = l_need_SmnSmn ? SmnSmn->const_array(mfi) : Array4<const Real>{};
 
        // **************************************************************************
        // Here we fill the "current" data with "new" data because that is the result of the previous RK stage
        // **************************************************************************
        int nsv = S_old[IntVars::cons].nComp() - 2;
        const GpuArray<int, IntVars::NumTypes> scomp_slow = {  2,0,0,0};
        const GpuArray<int, IntVars::NumTypes> ncomp_slow = {nsv,0,0,0};
 
        // **************************************************************************
        // Note that here we do copy only the "slow" variables, not (rho) or (rho theta)
        // **************************************************************************
        ParallelFor(tbx, ncomp_slow[IntVars::cons],
        [=] AMREX_GPU_DEVICE (int i, int j, int k, int nn) {
            const int n = scomp_slow[IntVars::cons] + nn;
            cur_cons(i,j,k,n) = new_cons(i,j,k,n);
        });
 
        // We have projected the velocities stored in S_data but we will use
        //    the velocities stored in {avg_xmom,avg_ymom,avg_zmom} to update the scalars,
        //    so we need to copy from S_data (projected) into these
        if (l_anelastic) {
            Box tbx_inc = mfi.nodaltilebox(0);
            Box tby_inc = mfi.nodaltilebox(1);
            Box tbz_inc = mfi.nodaltilebox(2);
 
            ParallelFor(tbx_inc, tby_inc, tbz_inc,
            [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept {
                avg_xmom_arr(i,j,k) = cur_xmom(i,j,k);
            },
            [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept {
                avg_ymom_arr(i,j,k) = cur_ymom(i,j,k);
            },
            [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept {
                avg_zmom_arr(i,j,k) = cur_zmom(i,j,k);
            });
        }
 
        // **************************************************************************
        // Define updates in the RHS of continuity, temperature, and scalar equations
        // **************************************************************************
        bool l_eb_terrain_cc = false; // EB terrain on cell-centered grid
        Array4<const int> mask_arr{};
        Array4<const EBCellFlag> cfg_arr{};
        Array4<const Real> ax_arr{};
        Array4<const Real> ay_arr{};
        Array4<const Real> az_arr{};
        Array4<const Real> fcx_arr{};
        Array4<const Real> fcy_arr{};
        Array4<const Real> fcz_arr{};
        Array4<const Real> detJ_arr{};
        if (solverChoice.terrain_type == TerrainType::EB) {
            EBCellFlagFab const& cfg = ebfact.getMultiEBCellFlagFab()[mfi];
            cfg_arr  = cfg.const_array();
            if (cfg.getType(tbx) == FabType::singlevalued) {
                l_eb_terrain_cc = true;
                ax_arr   = ebfact.getAreaFrac()[0]->const_array(mfi);
                ay_arr   = ebfact.getAreaFrac()[1]->const_array(mfi);
                az_arr   = ebfact.getAreaFrac()[2]->const_array(mfi);
                fcx_arr  = ebfact.getFaceCent()[0]->const_array(mfi);
                fcy_arr  = ebfact.getFaceCent()[1]->const_array(mfi);
                fcz_arr  = ebfact.getFaceCent()[2]->const_array(mfi);
                detJ_arr = ebfact.getVolFrac().const_array(mfi);
                // if (!already_on_centroids) {mask_arr = physbnd_mask.const_array(mfi);}
                mask_arr = physbnd_mask.const_array(mfi);
            }
        }
        if (!l_eb_terrain_cc) {
            ax_arr   = ax->const_array(mfi);
            ay_arr   = ay->const_array(mfi);
            az_arr   = az->const_array(mfi);
            detJ_arr = detJ->const_array(mfi);
        }
 
        AdvType horiz_adv_type, vert_adv_type;
        Real    horiz_upw_frac, vert_upw_frac;
 
        Array4<Real> diffflux_x, diffflux_y, diffflux_z;
        Array4<Real> hfx_x, hfx_y, hfx_z, diss;
        Array4<Real> q1fx_x, q1fx_y, q1fx_z, q2fx_z;
        const bool use_SurfLayer = (SurfLayer != nullptr);
 
        if (l_use_diff) {
            diffflux_x = dflux_x->array(mfi);
            diffflux_y = dflux_y->array(mfi);
            diffflux_z = dflux_z->array(mfi);
 
            hfx_x = Hfx1->array(mfi);
            hfx_y = Hfx2->array(mfi);
            hfx_z = Hfx3->array(mfi);
            diss  = Diss->array(mfi);
 
            if (Q1fx1) q1fx_x = Q1fx1->array(mfi);
            if (Q1fx2) q1fx_y = Q1fx2->array(mfi);
            if (Q1fx3) q1fx_z = Q1fx3->array(mfi);
            if (Q2fx3) q2fx_z = Q2fx3->array(mfi);
        }
 
        //
        // Note that we either advect and diffuse all or none of the moisture variables
        //
        for (int ivar(RhoKE_comp); ivar<= RhoQ1_comp; ++ivar)
        {
            if (is_valid_slow_var[ivar])
            {
                start_comp = ivar;
                num_comp = 1;
 
                if (ivar == RhoQ1_comp) {
                    horiz_adv_type = ac.moistscal_horiz_adv_type;
                     vert_adv_type = ac.moistscal_vert_adv_type;
                    horiz_upw_frac = ac.moistscal_horiz_upw_frac;
                     vert_upw_frac = ac.moistscal_vert_upw_frac;
 
                    if (ac.use_efficient_advection){
                         horiz_adv_type = EfficientAdvType(nrk,ac.moistscal_horiz_adv_type);
                          vert_adv_type = EfficientAdvType(nrk,ac.moistscal_vert_adv_type);
                    }
 
                    num_comp = n_qstate;
 
                } else {
                    horiz_adv_type = ac.dryscal_horiz_adv_type;
                     vert_adv_type = ac.dryscal_vert_adv_type;
                    horiz_upw_frac = ac.dryscal_horiz_upw_frac;
                     vert_upw_frac = ac.dryscal_vert_upw_frac;
 
                    if (ac.use_efficient_advection){
                         horiz_adv_type = EfficientAdvType(nrk,ac.dryscal_horiz_adv_type);
                          vert_adv_type = EfficientAdvType(nrk,ac.dryscal_vert_adv_type);
                    }
 
                    if (ivar == RhoScalar_comp) {
                        num_comp = NSCALARS;
                    }
                }
 
                if (( ivar != RhoKE_comp                 ) ||
                    ((ivar == RhoKE_comp) && l_advect_KE))
                {
                    if (!l_eb_terrain_cc){
                        AdvectionSrcForScalars(tbx, start_comp, num_comp,
                                               avg_xmom_arr, avg_ymom_arr, avg_zmom_arr,
                                               cur_prim, cell_rhs,
                                               detJ_arr, dxInv, mf_mx, mf_my,
                                               horiz_adv_type, vert_adv_type,
                                               horiz_upw_frac, vert_upw_frac,
                                               flx_arr, domain, bc_ptr_h);
                    } else {
                        EBAdvectionSrcForScalars(tbx, start_comp, num_comp,
                                                 avg_xmom_arr, avg_ymom_arr, avg_zmom_arr,
                                                 cur_prim, cell_rhs,
                                                 mask_arr, cfg_arr, ax_arr, ay_arr, az_arr,
                                                 fcx_arr, fcy_arr, fcz_arr,
                                                 detJ_arr, dxInv, mf_mx, mf_my,
                                                 horiz_adv_type, vert_adv_type,
                                                 horiz_upw_frac, vert_upw_frac,
                                                 flx_arr, domain, bc_ptr_h,
                                                 already_on_centroids);
                    }
                }
 
                if (l_use_diff)
                {
                    // Allow for implicit moisture diffusion
                    const Real l_vert_implicit_fac = (solverChoice.implicit_moisture_diffusion) ?
                                                     solverChoice.vert_implicit_fac[nrk] : zero;
 
                    const Array4<const Real> tm_arr = t_mean_mf ? t_mean_mf->const_array(mfi) : Array4<const Real>{};
 
                    if (solverChoice.mesh_type == MeshType::StretchedDz && solverChoice.terrain_type != TerrainType::EB) {
                        DiffusionSrcForState_S(tbx, domain, start_comp, num_comp, u, v,
                                               new_cons, cur_prim, cell_rhs,
                                               diffflux_x, diffflux_y, diffflux_z,
                                               stretched_dz_d, dxInv, SmnSmn_a,
                                               mf_mx, mf_ux, mf_vx,
                                               mf_my, mf_uy, mf_vy,
                                               hfx_z, q1fx_z, q2fx_z, diss,
                                               mu_turb, solverChoice, level,
                                               tm_arr, grav_gpu, bc_ptr_d, use_SurfLayer, l_vert_implicit_fac);
                    } else if (l_use_terrain) {
                        DiffusionSrcForState_T(tbx, domain, start_comp, num_comp, l_rotate, u, v,
                                               new_cons, cur_prim, cell_rhs,
                                               diffflux_x, diffflux_y, diffflux_z,
                                               z_nd, z_cc, ax_arr, ay_arr, az_arr,
                                               detJ_arr, dxInv, SmnSmn_a,
                                               mf_mx, mf_ux, mf_vx,
                                               mf_my, mf_uy, mf_vy,
                                               hfx_x, hfx_y, hfx_z, q1fx_x, q1fx_y, q1fx_z,q2fx_z, diss,
                                               mu_turb, solverChoice, level,
                                               tm_arr, grav_gpu, bc_ptr_d, use_SurfLayer, l_vert_implicit_fac);
                    } else {
                        DiffusionSrcForState_N(tbx, domain, start_comp, num_comp, u, v,
                                               new_cons, cur_prim, cell_rhs,
                                               diffflux_x, diffflux_y, diffflux_z, dxInv, SmnSmn_a,
                                               mf_mx, mf_ux, mf_vx,
                                               mf_my, mf_uy, mf_vy,
                                               hfx_z, q1fx_z, q2fx_z, diss,
                                               mu_turb, solverChoice, level,
                                               tm_arr, grav_gpu, bc_ptr_d, use_SurfLayer, l_vert_implicit_fac);
                    }
                } // use_diff
            } // valid slow var
        } // loop ivar
 
#if defined(ERF_USE_NETCDF)
        if (moist_set_rhs_bool)
        {
            Real bdy_factor = solverChoice.bdy_nudge_factor;
            const Array4<const Real> & new_cons_const = S_new[IntVars::cons].const_array(mfi);
            //
            // Note that old_stage_time_total = start_time+old_stage_time is total time
            //           start_bdy_time and final_bdy_time are total time
            //
            moist_set_rhs(geom, tbx, new_cons_const, cell_rhs,
                          old_stage_time_total, dt, start_bdy_time, final_bdy_time, bdy_time_interval,
                          bdy_factor, width, domain,
                          bdy_data_xlo, bdy_data_xhi,
                          bdy_data_ylo, bdy_data_yhi,
                          m_r2d);
        }
#endif
 
#ifdef ERF_USE_SHOC
        if (solverChoice.use_shoc) {
            shoc_lev->add_slow_tend(mfi,tbx,cell_rhs);
        }
#endif
 
        // This updates just the "slow" conserved variables
        {
        BL_PROFILE("rhs_post_8");
 
        const Real eps = std::numeric_limits<Real>::epsilon();
 
        auto const& src_arr = source.const_array(mfi);
 
        for (int ivar(RhoKE_comp); ivar<= RhoQ1_comp; ++ivar)
        {
            if (is_valid_slow_var[ivar])
            {
                start_comp = ivar;
                num_comp = 1;
                if (ivar == RhoQ1_comp) {
                    num_comp = nvars - RhoQ1_comp;
                } else if (ivar == RhoScalar_comp) {
                    num_comp = NSCALARS;
                }
 
               if (l_moving_terrain)
               {
                    ParallelFor(tbx, num_comp,
                    [=] AMREX_GPU_DEVICE (int i, int j, int k, int nn) noexcept {
                        const int n = start_comp + nn;
                        cell_rhs(i,j,k,n) += src_arr(i,j,k,n);
                        Real temp_val = detJ_arr(i,j,k) * old_cons(i,j,k,n) + dt * detJ_arr(i,j,k) * cell_rhs(i,j,k,n);
                        cur_cons(i,j,k,n) = temp_val / detJ_new_arr(i,j,k);
                        if (ivar == RhoKE_comp) {
                            cur_cons(i,j,k,n) = amrex::max(cur_cons(i,j,k,n), eps);
                        }
                    });
 
                } else if (l_anelastic && (nrk == 1)) { // not moving and ( (anelastic) and second RK stage) )
 
                    ParallelFor(tbx, num_comp,
                    [=] AMREX_GPU_DEVICE (int i, int j, int k, int nn) noexcept {
                        const int n = start_comp + nn;
                        cell_rhs(i,j,k,n) += src_arr(i,j,k,n);
 
                        // Re-construct the cell_rhs used in the first RK stage
                        Real dt_times_old_cell_rhs = cur_cons(i,j,k,n) - old_cons(i,j,k,n);
 
                        // Add the time-averaged RHS to the old state
                        cur_cons(i,j,k,n) = old_cons(i,j,k,n) + myhalf * (dt_times_old_cell_rhs + dt * cell_rhs(i,j,k,n));
 
                        if (ivar == RhoKE_comp) {
                            cur_cons(i,j,k,n) = amrex::max(cur_cons(i,j,k,n), eps);
                        } else if (ivar >= RhoQ1_comp) {
                            cur_cons(i,j,k,n) = amrex::max(cur_cons(i,j,k,n), amrex::Real(0));
                        }
                    });
 
                } else { // not moving and ( (not anelastic) or (first RK stage) )
 
                    ParallelFor(tbx, num_comp,
                    [=] AMREX_GPU_DEVICE (int i, int j, int k, int nn) noexcept {
                        const int n = start_comp + nn;
                        cell_rhs(i,j,k,n) += src_arr(i,j,k,n);
                        cur_cons(i,j,k,n) = old_cons(i,j,k,n) + dt * cell_rhs(i,j,k,n);
                        if (ivar == RhoKE_comp) {
                            cur_cons(i,j,k,n) = amrex::max(cur_cons(i,j,k,n), eps);
                        } else if (ivar >= RhoQ1_comp) {
                            cur_cons(i,j,k,n) = amrex::max(cur_cons(i,j,k,n), amrex::Real(0));
                        }
                    });
 
                } // moving, anelastic or neither?
 
            } // is_valid
        } // ivar
        } // profile
 
        {
        BL_PROFILE("rhs_post_9");
        // This updates all the conserved variables (not just the "slow" ones)
        int   num_comp_all = S_data[IntVars::cons].nComp();
        ParallelFor(tbx, num_comp_all,
        [=] AMREX_GPU_DEVICE (int i, int j, int k, int n) noexcept {
            new_cons(i,j,k,n)  = cur_cons(i,j,k,n);
        });
        } // end profile
 
        Box xtbx = mfi.nodaltilebox(0);
        Box ytbx = mfi.nodaltilebox(1);
        Box ztbx = mfi.nodaltilebox(2);
 
        {
        BL_PROFILE("rhs_post_10()");
        ParallelFor(xtbx, ytbx, ztbx,
        [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept {
            new_xmom(i,j,k) = cur_xmom(i,j,k);
        },
        [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept {
            new_ymom(i,j,k) = cur_ymom(i,j,k);
        },
        [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept {
            new_zmom(i,j,k) = cur_zmom(i,j,k);
        });
        } // end profile
 
        {
        BL_PROFILE("rhs_post_10");
        // We only add to the flux registers in the final RK step
        if (l_reflux) {
            int strt_comp_reflux = RhoTheta_comp + 1;
            int  num_comp_reflux = nvars - strt_comp_reflux;
            if (level < finest_level) {
                fr_as_crse->CrseAdd(mfi,
                    {{AMREX_D_DECL(&(flux[0]), &(flux[1]), &(flux[2]))}},
                    dx, dt, strt_comp_reflux, strt_comp_reflux, num_comp_reflux, RunOn::Device);
            }
            if (level > 0) {
                fr_as_fine->FineAdd(mfi,
                    {{AMREX_D_DECL(&(flux[0]), &(flux[1]), &(flux[2]))}},
                    dx, dt, strt_comp_reflux, strt_comp_reflux, num_comp_reflux, RunOn::Device);
            }
 
            // This is necessary here so we don't go on to the next FArrayBox without
            // having finished copying the fluxes into the FluxRegisters (since the fluxes
            // are stored in temporary FArrayBox's)
            Gpu::streamSynchronize();
 
        } // two-way coupling
        } // end profile
      } // mfi
    } // OMP
}

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