ERF_MakeSources.cpp File Reference

#include <AMReX_MultiFab.H>
#include <AMReX_ArrayLim.H>
#include <AMReX_BCRec.H>
#include <AMReX_TableData.H>
#include <AMReX_GpuContainers.H>
#include <ERF_NumericalDiffusion.H>
#include <ERF_PlaneAverage.H>
#include <ERF_SrcHeaders.H>
#include <ERF_TI_slow_headers.H>
#include <ERF_MOSTStress.H>

Include dependency graph for ERF_MakeSources.cpp:

Functions
void	make_sources (int level, int, Real dt, Real time, const Vector< MultiFab > &S_data, const MultiFab &S_prim, MultiFab &source, const MultiFab &base_state, const MultiFab *z_phys_cc, const MultiFab &xvel, const MultiFab &yvel, const MultiFab *qheating_rates, MultiFab *terrain_blank, const Geometry geom, const SolverChoice &solverChoice, Vector< std::unique_ptr< MultiFab >> &mapfac, const MultiFab *rhotheta_src, const MultiFab *rhoqt_src, const Real *dptr_wbar_sub, const Vector< Real * > d_rayleigh_ptrs_at_lev, const Real *d_sinesq_at_lev, const MultiFab *surface_state_at_lev, InputSoundingData &input_sounding_data, TurbulentPerturbation &turbPert, bool is_slow_step)

Function Documentation

make_sources()

void make_sources	(	int	level,
		int	,
		Real	dt,
		Real	time,
		const Vector< MultiFab > &	S_data,
		const MultiFab &	S_prim,
		MultiFab &	source,
		const MultiFab &	base_state,
		const MultiFab *	z_phys_cc,
		const MultiFab &	xvel,
		const MultiFab &	yvel,
		const MultiFab *	qheating_rates,
		MultiFab *	terrain_blank,
		const Geometry	geom,
		const SolverChoice &	solverChoice,
		Vector< std::unique_ptr< MultiFab >> &	mapfac,
		const MultiFab *	rhotheta_src,
		const MultiFab *	rhoqt_src,
		const Real *	dptr_wbar_sub,
		const Vector< Real * >	d_rayleigh_ptrs_at_lev,
		const Real *	d_sinesq_at_lev,
		const MultiFab *	surface_state_at_lev,
		InputSoundingData &	input_sounding_data,
		TurbulentPerturbation &	turbPert,
		bool	is_slow_step
	)

Function for computing the slow RHS for the evolution equations for the density, potential temperature and momentum.

Parameters

[in]	level	level of resolution
[in]	nrk	which RK stage
[in]	dt	slow time step
[in]	S_data	current solution
[in]	S_prim	primitive variables (i.e. conserved variables divided by density)
[in]	source	source terms for conserved variables
[in]	geom	Container for geometric information
[in]	solverChoice	Container for solver parameters
[in]	mapfac	map factors
[in]	dptr_rhotheta_src	custom temperature source term
[in]	dptr_rhoqt_src	custom moisture source term
[in]	dptr_wbar_sub	subsidence source term
[in]	d_rayleigh_ptrs_at_lev	Vector of {strength of Rayleigh damping, reference value of theta} used to define Rayleigh damping
[in]	d_sinesq_at_lev	sin( (pi/2) (z-z_t)/(damping depth)) at cell centers

{
    BL_PROFILE_REGION("erf_make_sources()");
 
    // *****************************************************************************
    // Initialize source to zero since we re-compute it every RK stage
    // *****************************************************************************
    if (is_slow_step) {
        source.setVal(0.);
    } else {
        source.setVal(0.0,Rho_comp,2);
    }
 
    const bool l_use_ndiff      = solverChoice.use_num_diff;
 
    TurbChoice tc = solverChoice.turbChoice[level];
    const bool l_use_KE  = tc.use_tke;
    const bool l_diff_KE = tc.diffuse_tke_3D;
 
    const Box& domain = geom.Domain();
 
    const GpuArray<Real, AMREX_SPACEDIM> dxInv = geom.InvCellSizeArray();
    const GpuArray<Real, AMREX_SPACEDIM> dx    = geom.CellSizeArray();
 
    MultiFab r_hse (base_state, make_alias, BaseState::r0_comp , 1);
    MultiFab th_hse (base_state, make_alias, BaseState::th0_comp , 1);
    MultiFab qv_hse (base_state, make_alias, BaseState::qv0_comp , 1);
 
    Real* thetabar = d_rayleigh_ptrs_at_lev[Rayleigh::thetabar];
 
    // flags to apply certain source terms in substep call only
    bool use_Rayleigh_fast = ( (solverChoice.dampingChoice.rayleigh_damping_type == RayleighDampingType::FastExplicit) ||
                               (solverChoice.dampingChoice.rayleigh_damping_type == RayleighDampingType::FastImplicit) );
    bool use_ImmersedForcing_fast = solverChoice.immersed_forcing_substep;
 
    // flag for a moisture model
    bool has_moisture = (solverChoice.moisture_type != MoistureType::None);
 
    // *****************************************************************************
    // Planar averages for subsidence terms
    // *****************************************************************************
    Table1D<Real>      dptr_r_plane, dptr_t_plane, dptr_qv_plane, dptr_qc_plane;
    TableData<Real, 1>  r_plane_tab,  t_plane_tab,  qv_plane_tab,  qc_plane_tab;
    bool compute_averages = ( is_slow_step && (dptr_wbar_sub || solverChoice.nudging_from_input_sounding) );
 
    if (compute_averages)
    {
        // The plane averaging operates at fixed z not fixed height so is not correct for variable dz
        AMREX_ALWAYS_ASSERT(solverChoice.mesh_type != MeshType::VariableDz);
 
        //
        // The call to "compute_averages" currently does all the components in one call
        // We can then extract each component separately with the "line_average" call
        //
        // We need just one ghost cell in the vertical
        //
        IntVect ng_c(S_data[IntVars::cons].nGrowVect()); ng_c[2] = 1;
        //
        // With no moisture we only (rho) and (rho theta); with moisture we also do qv and qc
        // We use the alias here to control ncomp inside the PlaneAverage
        //
        int ncomp = (!has_moisture) ? 2 : RhoQ2_comp+1;
        MultiFab cons(S_data[IntVars::cons], make_alias, 0, ncomp);
 
        PlaneAverage cons_ave(&cons, geom, solverChoice.ave_plane, ng_c);
        cons_ave.compute_averages(ZDir(), cons_ave.field());
 
        int ncell = cons_ave.ncell_line();
 
        Gpu::HostVector<    Real> r_plane_h(ncell);
        Gpu::DeviceVector<  Real> r_plane_d(ncell);
 
        Gpu::HostVector<    Real> t_plane_h(ncell);
        Gpu::DeviceVector<  Real> t_plane_d(ncell);
 
        cons_ave.line_average(Rho_comp     , r_plane_h);
        cons_ave.line_average(RhoTheta_comp, t_plane_h);
 
        Gpu::copyAsync(Gpu::hostToDevice, r_plane_h.begin(), r_plane_h.end(), r_plane_d.begin());
        Gpu::copyAsync(Gpu::hostToDevice, t_plane_h.begin(), t_plane_h.end(), t_plane_d.begin());
 
        Real* dptr_r = r_plane_d.data();
        Real* dptr_t = t_plane_d.data();
 
        Box tdomain  = domain; tdomain.grow(2,ng_c[2]);
        r_plane_tab.resize({tdomain.smallEnd(2)}, {tdomain.bigEnd(2)});
        t_plane_tab.resize({tdomain.smallEnd(2)}, {tdomain.bigEnd(2)});
 
        int offset = ng_c[2];
 
        dptr_r_plane = r_plane_tab.table();
        dptr_t_plane = t_plane_tab.table();
        ParallelFor(ncell, [=] AMREX_GPU_DEVICE (int k) noexcept
        {
            dptr_r_plane(k-offset) = dptr_r[k];
            dptr_t_plane(k-offset) = dptr_t[k];
        });
 
        if (has_moisture)
        {
            Gpu::HostVector<  Real> qv_plane_h(ncell), qc_plane_h(ncell);
            Gpu::DeviceVector<Real> qv_plane_d(ncell), qc_plane_d(ncell);
 
            // Water vapor
            cons_ave.line_average(RhoQ1_comp, qv_plane_h);
            Gpu::copyAsync(Gpu::hostToDevice, qv_plane_h.begin(), qv_plane_h.end(), qv_plane_d.begin());
 
            // Cloud water
            cons_ave.line_average(RhoQ2_comp, qc_plane_h);
            Gpu::copyAsync(Gpu::hostToDevice, qc_plane_h.begin(), qc_plane_h.end(), qc_plane_d.begin());
 
            Real* dptr_qv = qv_plane_d.data();
            Real* dptr_qc = qc_plane_d.data();
 
            qv_plane_tab.resize({tdomain.smallEnd(2)}, {tdomain.bigEnd(2)});
            qc_plane_tab.resize({tdomain.smallEnd(2)}, {tdomain.bigEnd(2)});
 
            dptr_qv_plane = qv_plane_tab.table();
            dptr_qc_plane = qc_plane_tab.table();
            ParallelFor(ncell, [=] AMREX_GPU_DEVICE (int k) noexcept
            {
                dptr_qv_plane(k-offset) = dptr_qv[k];
                dptr_qc_plane(k-offset) = dptr_qc[k];
            });
        }
    }
 
    // *****************************************************************************
    // Radiation flux vector for four stream approximation
    // *****************************************************************************
    // NOTE: The fluxes live on w-faces
    int klo = domain.smallEnd(0);
    int khi = domain.bigEnd(2);
    int nk  = khi - klo + 2;
    Gpu::DeviceVector<Real> radiation_flux(nk,zero);
    Gpu::DeviceVector<Real> q_integral(nk,zero);
    Real* rad_flux = radiation_flux.data();
    Real* q_int    = q_integral.data();
 
    // *****************************************************************************
    // Define source term for cell-centered conserved variables, from
    //    one user-defined source terms for (rho theta) and (rho q_t)
    //    two radiation           for (rho theta)
    //    three Rayleigh damping    for (rho theta)
    //    Real(4.) custom forcing      for (rho theta) and (rho Q1)
    //    Real(5.) custom subsidence   for (rho theta) and (rho Q1)
    //    Real(6.) numerical diffusion for (rho theta)
    //    Real(7.) sponging
    //    Real(8.) turbulent perturbation
    //    Real(9.) nudging towards input sounding values (only for theta)
    //   10a. Immersed forcing for terrain
    //   10b. Immersed forcing for buildings
    //   Real(11.) Four stream radiation source for (rho theta)
    // *****************************************************************************
 
    // ***********************************************************************************************
    // Add remaining source terms
    // ***********************************************************************************************
#ifdef _OPENMP
#pragma omp parallel if (Gpu::notInLaunchRegion())
#endif
    {
    for ( MFIter mfi(S_data[IntVars::cons],TileNoZ()); mfi.isValid(); ++mfi)
    {
        Box bx  = mfi.tilebox();
 
        const Array4<const Real>& cell_data  = S_data[IntVars::cons].array(mfi);
        const Array4<const Real>& cell_prim  = S_prim.array(mfi);
        const Array4<Real>      & cell_src   = source.array(mfi);
 
        const Array4<const Real>& r0 = r_hse.const_array(mfi);
        const Array4<const Real>& th0 = th_hse.const_array(mfi);
        const Array4<const Real>& qv0 = qv_hse.const_array(mfi);
 
        const Array4<const Real>& z_cc_arr = z_phys_cc->const_array(mfi);
 
        const Array4<const Real>& t_blank_arr = (terrain_blank) ? terrain_blank->const_array(mfi) :
                                                               Array4<const Real>{};
 
 
        // *************************************************************************************
        // two Add radiation source terms to (rho theta)
        // *************************************************************************************
        if (solverChoice.rad_type != RadiationType::None && is_slow_step) {
            auto const& qheating_arr = qheating_rates->const_array(mfi);
            ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
            {
                // Short-wavelength and long-wavelength radiation source terms
                cell_src(i,j,k,RhoTheta_comp) += cell_data(i,j,k,Rho_comp) * ( qheating_arr(i,j,k,0) + qheating_arr(i,j,k,1) );
            });
        }
 
 
        // *************************************************************************************
        // three Add Rayleigh damping for (rho theta)
        // *************************************************************************************
        Real dampcoef = solverChoice.dampingChoice.rayleigh_dampcoef;
 
        if (solverChoice.dampingChoice.rayleigh_damp_T) {
            if ((is_slow_step && !use_Rayleigh_fast) || (!is_slow_step && use_Rayleigh_fast)) {
                int n  = RhoTheta_comp;
                int nr = Rho_comp;
                int np = PrimTheta_comp;
 
                ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                {
                    Real theta = cell_prim(i,j,k,np);
                    Real sinesq = d_sinesq_at_lev[k];
                    cell_src(i, j, k, n) -= dampcoef*sinesq * (theta - thetabar[k]) * cell_data(i,j,k,nr);
                });
            }
        }
 
        // *************************************************************************************
        // Real(4.) Add custom forcing for (rho theta)
        // *************************************************************************************
        if (solverChoice.custom_rhotheta_forcing && is_slow_step) {
            const int n = RhoTheta_comp;
            auto const& rhotheta_src_arr = rhotheta_src->const_array(mfi);
            if (solverChoice.spatial_rhotheta_forcing)
            {
                if (solverChoice.custom_forcing_prim_vars) {
                    const int nr = Rho_comp;
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += cell_data(i,j,k,nr) * rhotheta_src_arr(i, j, k);
                    });
                } else {
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += rhotheta_src_arr(i, j, k);
                    });
                }
            } else {
                if (solverChoice.custom_forcing_prim_vars) {
                    const int nr = Rho_comp;
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += cell_data(i,j,k,nr) * rhotheta_src_arr(0, 0, k);
                    });
                } else {
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += rhotheta_src_arr(0, 0, k);
                    });
                }
            }
        }
 
        // *************************************************************************************
        // Real(4.) Add custom forcing for RhoQ1
        // *************************************************************************************
        if (solverChoice.custom_moisture_forcing && is_slow_step) {
            const int n = RhoQ1_comp;
            auto const& rhoqt_src_arr = rhoqt_src->const_array(mfi);
            if (solverChoice.spatial_moisture_forcing)
            {
                if (solverChoice.custom_forcing_prim_vars) {
                    const int nr = Rho_comp;
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += cell_data(i,j,k,nr) * rhoqt_src_arr(i, j, k);
                    });
                } else {
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += rhoqt_src_arr(i, j, k);
                    });
                }
            } else {
                if (solverChoice.custom_forcing_prim_vars) {
                    const int nr = Rho_comp;
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += cell_data(i,j,k,nr) * rhoqt_src_arr(0, 0, k);
                    });
                } else {
                    ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                    {
                        cell_src(i, j, k, n) += rhoqt_src_arr(0, 0, k);
                    });
                }
            }
        }
 
        // *************************************************************************************
        // Real(5.) Add custom subsidence for (rho theta)
        // *************************************************************************************
        if (solverChoice.custom_w_subsidence && is_slow_step && solverChoice.do_theta_advection) {
            const int n = RhoTheta_comp;
            if (solverChoice.custom_forcing_prim_vars) {
                const int nr = Rho_comp;
                ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                {
                    Real dzInv = (z_cc_arr) ? one/ (z_cc_arr(i,j,k+1) - z_cc_arr(i,j,k-1)) : myhalf*dxInv[2];
                    Real T_hi = dptr_t_plane(k+1) / dptr_r_plane(k+1);
                    Real T_lo = dptr_t_plane(k-1) / dptr_r_plane(k-1);
                    Real wbar_cc = myhalf * (dptr_wbar_sub[k] + dptr_wbar_sub[k+1]);
                    cell_src(i, j, k, n) -= cell_data(i,j,k,nr) * wbar_cc * (T_hi - T_lo) * dzInv;
                });
            } else {
                ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                {
                    Real dzInv = (z_cc_arr) ? one/ (z_cc_arr(i,j,k+1) - z_cc_arr(i,j,k-1)) : myhalf*dxInv[2];
                    Real T_hi = dptr_t_plane(k+1) / dptr_r_plane(k+1);
                    Real T_lo = dptr_t_plane(k-1) / dptr_r_plane(k-1);
                    Real wbar_cc = myhalf * (dptr_wbar_sub[k] + dptr_wbar_sub[k+1]);
                    cell_src(i, j, k, n) -= wbar_cc * (T_hi - T_lo) * dzInv;
                });
            }
        }
 
        // *************************************************************************************
        // Real(5.) Add custom subsidence for RhoQ1 and RhoQ2
        // *************************************************************************************
        if (solverChoice.custom_w_subsidence && (solverChoice.moisture_type != MoistureType::None) && is_slow_step) {
            const int nv = RhoQ1_comp;
            if (solverChoice.custom_forcing_prim_vars) {
                const int nr = Rho_comp;
                ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                {
                    Real dzInv = (z_cc_arr) ? one/ (z_cc_arr(i,j,k+1) - z_cc_arr(i,j,k-1)) : myhalf*dxInv[2];
                    Real Qv_hi = dptr_qv_plane(k+1) / dptr_r_plane(k+1);
                    Real Qv_lo = dptr_qv_plane(k-1) / dptr_r_plane(k-1);
                    Real Qc_hi = dptr_qc_plane(k+1) / dptr_r_plane(k+1);
                    Real Qc_lo = dptr_qc_plane(k-1) / dptr_r_plane(k-1);
                    Real wbar_cc = myhalf * (dptr_wbar_sub[k] + dptr_wbar_sub[k+1]);
                    cell_src(i, j, k, nv  ) -= cell_data(i,j,k,nr) * wbar_cc * (Qv_hi - Qv_lo) * dzInv;
                    cell_src(i, j, k, nv+1) -= cell_data(i,j,k,nr) * wbar_cc * (Qc_hi - Qc_lo) * dzInv;
                });
            } else {
                ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
                {
                    Real dzInv = (z_cc_arr) ? one/ (z_cc_arr(i,j,k+1) - z_cc_arr(i,j,k-1)) : myhalf*dxInv[2];
                    Real Qv_hi = dptr_qv_plane(k+1) / dptr_r_plane(k+1);
                    Real Qv_lo = dptr_qv_plane(k-1) / dptr_r_plane(k-1);
                    Real Qc_hi = dptr_qc_plane(k+1) / dptr_r_plane(k+1);
                    Real Qc_lo = dptr_qc_plane(k-1) / dptr_r_plane(k-1);
                    Real wbar_cc = myhalf * (dptr_wbar_sub[k] + dptr_wbar_sub[k+1]);
                    cell_src(i, j, k, nv  ) -= wbar_cc * (Qv_hi - Qv_lo) * dzInv;
                    cell_src(i, j, k, nv+1) -= wbar_cc * (Qc_hi - Qc_lo) * dzInv;
                });
            }
        }
 
        // *************************************************************************************
        // Real(6.) Add numerical diffusion for rho and (rho theta)
        // *************************************************************************************
        if (l_use_ndiff && is_slow_step)
        {
            const Array4<const Real>& mf_mx   = mapfac[MapFacType::m_x]->const_array(mfi);
            const Array4<const Real>& mf_my   = mapfac[MapFacType::m_y]->const_array(mfi);
 
            // Rho is a special case
            NumericalDiffusion_Scal(bx, 0, 1, dt, solverChoice.num_diff_coeff,
                                    cell_data, cell_data, cell_src, mf_mx, mf_my);
 
            // Other scalars proceed as normal
            NumericalDiffusion_Scal(bx, 1, 1, dt, solverChoice.num_diff_coeff,
                                    cell_prim, cell_data, cell_src, mf_mx, mf_my);
 
 
            if (l_use_KE && l_diff_KE) {
                NumericalDiffusion_Scal(bx, RhoKE_comp, 1, dt, solverChoice.num_diff_coeff,
                                        cell_prim, cell_data, cell_src, mf_mx, mf_my);
            }
 
            NumericalDiffusion_Scal(bx, RhoScalar_comp, NSCALARS, dt, solverChoice.num_diff_coeff,
                                    cell_prim, cell_data, cell_src, mf_mx, mf_my);
        }
 
        // *************************************************************************************
        // Real(7.) Add sponging
        // *************************************************************************************
        if (!(solverChoice.spongeChoice.sponge_type == SpongeType::Input_Sponge) && is_slow_step){
            const int n_qstate = S_data[IntVars::cons].nComp() - (NDRY + NSCALARS);
            ApplySpongeZoneBCsForCC(solverChoice.spongeChoice, geom, bx, cell_src, cell_data, r0, th0, qv0, z_cc_arr, n_qstate);
        }
 
        if (solverChoice.init_type == InitType::HindCast and solverChoice.hindcast_surface_bcs) {
            const Array4<const Real>& surface_state_arr = (*surface_state_at_lev).array(mfi);
            ApplySurfaceTreatment_BulkCoeff_CC(bx, cell_src, cell_data, z_cc_arr, surface_state_arr);
        }
 
 
        // *************************************************************************************
        // Real(8.) Add perturbation
        // *************************************************************************************
        if (solverChoice.use_source_perturbation(level) && is_slow_step) {
            auto m_ixtype = S_data[IntVars::cons].boxArray().ixType(); // Conserved term
            const amrex::Array4<const amrex::Real>& pert_cell = turbPert.pb_cell[level].const_array(mfi);
            turbPert.apply_tpi(level, bx, RhoTheta_comp, m_ixtype, cell_src, pert_cell); // Applied as source term
        }
 
        // *************************************************************************************
        // Real(9.) Add nudging towards value specified in input sounding
        // *************************************************************************************
        if (solverChoice.nudging_from_input_sounding && is_slow_step)
        {
            int itime_n    = 0;
            int itime_np1  = 0;
            Real coeff_n   = one;
            Real coeff_np1 = zero;
 
            Real tau_inv = one / input_sounding_data.tau_nudging;
 
            int n_sounding_times = input_sounding_data.input_sounding_time.size();
 
            for (int nt = 1; nt < n_sounding_times; nt++) {
                if (time > input_sounding_data.input_sounding_time[nt]) itime_n = nt;
            }
            if (itime_n == n_sounding_times-1) {
                itime_np1 = itime_n;
            } else {
                itime_np1 = itime_n+1;
                coeff_np1 = (time                                               - input_sounding_data.input_sounding_time[itime_n]) /
                            (input_sounding_data.input_sounding_time[itime_np1] - input_sounding_data.input_sounding_time[itime_n]);
                coeff_n   = one - coeff_np1;
            }
 
            const Real* theta_inp_sound_n   = input_sounding_data.theta_inp_sound_d[itime_n].dataPtr();
            const Real* theta_inp_sound_np1 = input_sounding_data.theta_inp_sound_d[itime_np1].dataPtr();
 
            const int n  = RhoTheta_comp;
            const int nr = Rho_comp;
 
            ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
            {
                Real nudge = (coeff_n*theta_inp_sound_n[k] + coeff_np1*theta_inp_sound_np1[k]) - (dptr_t_plane(k)/dptr_r_plane(k));
                nudge *= tau_inv;
                cell_src(i, j, k, n) += cell_data(i, j, k, nr) * nudge;
            });
        }
 
        // *************************************************************************************
        // 10a. Add immersed source terms for terrain
        // *************************************************************************************
        if (solverChoice.terrain_type == TerrainType::ImmersedForcing &&
           ((is_slow_step && !use_ImmersedForcing_fast) || (!is_slow_step && use_ImmersedForcing_fast)))
        {
            const Array4<const Real>& u = xvel.array(mfi);
            const Array4<const Real>& v = yvel.array(mfi);
 
            // geometric properties
            const Real* dx_arr = geom.CellSize();
            const Real dx_x = dx_arr[0];
            const Real dx_y = dx_arr[1];
            const Real dx_z = dx_arr[2];
 
            const Real alpha_h          = solverChoice.if_Cd_scalar;
            const Real drag_coefficient = alpha_h / std::pow(dx_x*dx_y*dx_z, one/three);
            const Real tiny             = std::numeric_limits<amrex::Real>::epsilon();
            const Real U_s              = one; // unit velocity scale
 
            // MOST parameters
            similarity_funs sfuns;
            const Real ggg                = CONST_GRAV;
            const Real kappa              = KAPPA;
            const Real z0                 = solverChoice.if_z0;
            const Real tflux              = solverChoice.if_surf_temp_flux;
            const Real init_surf_temp     = solverChoice.if_init_surf_temp;
 
            // Note this has been converted to K / s when it was read in;
            const Real surf_heating_rate  = solverChoice.if_surf_heating_rate;
 
            const Real Olen_in            = solverChoice.if_Olen_in;
 
            ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k) noexcept
            {
                const Real t_blank       = t_blank_arr(i, j, k);
                const Real t_blank_above = t_blank_arr(i, j, k+1);
                const Real ux_cc_2r = myhalf * (u(i  ,j  ,k+1) + u(i+1,j  ,k+1));
                const Real uy_cc_2r = myhalf * (v(i  ,j  ,k+1) + v(i  ,j+1,k+1));
                const Real h_windspeed2r  = std::sqrt(ux_cc_2r * ux_cc_2r + uy_cc_2r * uy_cc_2r);
 
                const Real theta          = cell_data(i,j,k  ,RhoTheta_comp) / cell_data(i,j,k  ,Rho_comp);
                const Real theta_neighbor = cell_data(i,j,k+1,RhoTheta_comp) / cell_data(i,j,k+1,Rho_comp);
 
                // SURFACE TEMP AND HEATING/COOLING RATE
                if (init_surf_temp > zero) {
                    if (t_blank > 0 && (t_blank_above == zero)) { // force to MOST value
                        const Real surf_temp    = init_surf_temp + surf_heating_rate*time;
                        const Real bc_forcing_rt_srf = -(cell_data(i,j,k-1,Rho_comp) * surf_temp - cell_data(i,j,k-1,RhoTheta_comp));
                        cell_src(i, j, k-1, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt_srf; // k-1
                    }
                }
 
                // SURFACE HEAT FLUX
                if (tflux != Real(1e-8)){
                    if (t_blank > 0 && (t_blank_above == zero)) { // force to MOST value
                        Real psi_m           = zero;
                        Real psi_h           = zero;
                        Real psi_h_neighbor  = zero;
                        Real ustar = h_windspeed2r * kappa / (std::log((Real(1.5)) * dx_z / z0) - psi_m);
                        const Real Olen  = -ustar * ustar * ustar * theta / (kappa * ggg * tflux + tiny);
                        const Real zeta          = (myhalf) * dx_z / Olen;
                        const Real zeta_neighbor = (Real(1.5)) * dx_z / Olen;
 
                        // similarity functions
                        psi_m          = sfuns.calc_psi_m(zeta);
                        psi_h          = sfuns.calc_psi_h(zeta);
                        psi_h_neighbor = sfuns.calc_psi_h(zeta_neighbor);
                        ustar = h_windspeed2r * kappa / (std::log((Real(1.5)) * dx_z / z0) - psi_m);
 
                        // prevent some unphysical math
                        if (!(ustar > zero && !std::isnan(ustar))) { ustar = zero; }
                        if (!(ustar < two && !std::isnan(ustar))) { ustar = two; }
                        if (psi_h_neighbor > std::log(Real(1.5) * dx_z / z0)) { psi_h_neighbor = std::log(Real(1.5) * dx_z / z0); }
                        if (psi_h > std::log(myhalf * dx_z / z0)) { psi_h = std::log(myhalf * dx_z / z0); }
 
                        // We do not know the actual temperature so use cell above
                        const Real thetastar    = theta * ustar * ustar / (kappa * ggg * Olen);
                        const Real surf_temp    = theta_neighbor - thetastar / kappa * (std::log((Real(1.5)) * dx_z / z0) - psi_h_neighbor);
                        const Real tTarget      = surf_temp + thetastar / kappa * (std::log((myhalf) * dx_z / z0) - psi_h);
 
                        const Real bc_forcing_rt = -(cell_data(i,j,k,Rho_comp) * tTarget - cell_data(i,j,k,RhoTheta_comp));
                        cell_src(i, j, k, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt;
                    }
                }
 
                // OBUKHOV LENGTH
                if (Olen_in != Real(1e-8)){
                    if (t_blank > 0 && (t_blank_above == zero)) { // force to MOST value
                        const Real Olen  = Olen_in;
                        const Real zeta          = (myhalf) * dx_z / Olen;
                        const Real zeta_neighbor = (Real(1.5)) * dx_z / Olen;
 
                        // similarity functions
                        const Real psi_m          = sfuns.calc_psi_m(zeta);
                        const Real psi_h          = sfuns.calc_psi_h(zeta);
                        const Real psi_h_neighbor = sfuns.calc_psi_h(zeta_neighbor);
                        const Real ustar = h_windspeed2r * kappa / (std::log((Real(1.5)) * dx_z / z0) - psi_m);
 
                        // We do not know the actual temperature so use cell above
                        const Real thetastar    = theta * ustar * ustar / (kappa * ggg * Olen);
                        const Real surf_temp    = theta_neighbor - thetastar / kappa * (std::log((Real(1.5)) * dx_z / z0) - psi_h_neighbor);
                        const Real tTarget      = surf_temp + thetastar / kappa * (std::log((myhalf) * dx_z / z0) - psi_h);
 
                        const Real bc_forcing_rt = -(cell_data(i,j,k,Rho_comp) * tTarget - cell_data(i,j,k,RhoTheta_comp));
                        cell_src(i, j, k, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt;
                    }
                }
 
            });
        }
 
        // *************************************************************************************
        // 10b. Add immersed source terms for buildings
        // *************************************************************************************
        if ((solverChoice.buildings_type == BuildingsType::ImmersedForcing ) &&
           ((is_slow_step && !use_ImmersedForcing_fast) || (!is_slow_step && use_ImmersedForcing_fast)))
        {
            // geometric properties
            const Real* dx_arr = geom.CellSize();
            const Real dx_x = dx_arr[0];
            const Real dx_y = dx_arr[1];
 
            const Real alpha_h          = solverChoice.if_Cd_scalar;
            const Real U_s              = one; // unit velocity scale
            const Real min_t_blank      = Real(0.005);
 
            const Real init_surf_temp     = solverChoice.if_init_surf_temp;
 
            // Note this has been converted to K / s when it was read in;
            const Real surf_heating_rate  = solverChoice.if_surf_heating_rate;
 
            ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k) noexcept
            {
                Real t_blank       = t_blank_arr(i, j, k);
                Real t_blank_below = t_blank_arr(i, j, k-1);
                Real t_blank_above = t_blank_arr(i, j, k+1);
                Real t_blank_north  = t_blank_arr(i  , j+1, k);
                Real t_blank_south  = t_blank_arr(i  , j-1, k);
                Real t_blank_east   = t_blank_arr(i+1, j  , k);
                Real t_blank_west   = t_blank_arr(i-1, j  , k);
                if (t_blank < min_t_blank) { t_blank = zero; } // deal with situations where very small volfrac exist
                if (t_blank_below < min_t_blank) { t_blank_below = zero; }
                if (t_blank_north < min_t_blank) { t_blank_north = zero; }
                if (t_blank_south < min_t_blank) { t_blank_south = zero; }
                if (t_blank_east < min_t_blank) { t_blank_east = zero; }
                if (t_blank_west < min_t_blank) { t_blank_west = zero; }
 
                Real dx_z    = (z_cc_arr) ? (z_cc_arr(i,j,k) - z_cc_arr(i,j,k-1)) : dx[2];
                Real drag_coefficient = alpha_h / std::pow(dx_x*dx_y*dx_z, one/three);
 
                // SURFACE TEMP AND HEATING/COOLING RATE
                if (init_surf_temp > zero) {
                    const Real surf_temp    = init_surf_temp + surf_heating_rate*time;
                    if (t_blank > 0 && (t_blank_above == zero) && (t_blank_below == one)) { // building roof
                        const Real bc_forcing_rt_srf = -(cell_data(i,j,k,Rho_comp) * surf_temp - cell_data(i,j,k,RhoTheta_comp));
                        cell_src(i, j, k, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt_srf;
 
                    } else if (((t_blank > 0 && t_blank < t_blank_west && t_blank_east == zero) ||
                                (t_blank > 0 && t_blank < t_blank_east && t_blank_west == zero) ||
                                (t_blank > 0 && t_blank < t_blank_north && t_blank_south == zero) ||
                                (t_blank > 0 && t_blank < t_blank_south && t_blank_north == zero))) {
                        // this should enter for just building walls
                        // walls are currently separated to allow for flexible in the future to heat walls differently
 
                        // south face
                        if ((t_blank < t_blank_north) && (t_blank_north == one)) {
                            const Real bc_forcing_rt_srf = -(cell_data(i,j,k,Rho_comp) * surf_temp - cell_data(i,j,k,RhoTheta_comp));
                            cell_src(i, j, k, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt_srf;
                        }
 
                        // north face
                        if ((t_blank < t_blank_south) && (t_blank_south == one)) {
                            const Real bc_forcing_rt_srf = -(cell_data(i,j,k,Rho_comp) * surf_temp - cell_data(i,j,k,RhoTheta_comp));
                            cell_src(i, j, k, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt_srf;
                        }
 
                        // west face
                        if ((t_blank < t_blank_east) && (t_blank_east == one)) {
                            const Real bc_forcing_rt_srf = -(cell_data(i,j,k,Rho_comp) * surf_temp - cell_data(i,j,k,RhoTheta_comp));
                            cell_src(i, j, k, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt_srf;
                        }
 
                        // east face
                        if ((t_blank < t_blank_west) && (t_blank_west == one)) {
                            const Real bc_forcing_rt_srf = -(cell_data(i,j,k,Rho_comp) * surf_temp - cell_data(i,j,k,RhoTheta_comp));
                            cell_src(i, j, k, RhoTheta_comp) -= drag_coefficient * U_s * bc_forcing_rt_srf;
                        }
 
                    }
                }
            });
        }
 
        // *************************************************************************************
        // Real(11.) Add 4 stream radiation src to RhoTheta
        // *************************************************************************************
        if (solverChoice.four_stream_radiation && has_moisture && is_slow_step)
        {
            AMREX_ALWAYS_ASSERT((bx.smallEnd(2) == klo) && (bx.bigEnd(2) == khi));
            Real D    = Real(3.75e-6); // [s^-1]
            Real F0   = 70;      // [W/m^2]
            Real F1   = 22;      // [W/m^2]
            Real krad = 85;      // [m^2 kg^-1]
            Real qt_i = Real(0.008);
 
            Box xybx = makeSlab(bx,2,klo);
            ParallelFor(xybx, [=] AMREX_GPU_DEVICE(int i, int j, int /*k*/) noexcept
            {
                // Inclusive scan at w-faces for the Q integral (also find "i" values)
                q_int[0] = zero;
                Real zi   = myhalf * (z_cc_arr(i,j,khi) + z_cc_arr(i,j,khi-1));
                Real rhoi = myhalf * (cell_data(i,j,khi,Rho_comp) + cell_data(i,j,khi-1,Rho_comp));
                for (int k(klo+1); k<=khi+1; ++k) {
                    int lk    = k - klo;
                    // Average to w-faces when looping w-faces
                    Real dz    = (z_cc_arr) ? myhalf * (z_cc_arr(i,j,k) - z_cc_arr(i,j,k-2)) : dx[2];
                    q_int[lk]  = q_int[lk-1] + krad * cell_data(i,j,k-1,Rho_comp) * cell_data(i,j,k-1,RhoQ2_comp) * dz;
                    Real qt_hi = cell_data(i,j,k  ,RhoQ1_comp) + cell_data(i,j,k  ,RhoQ2_comp);
                    Real qt_lo = cell_data(i,j,k-1,RhoQ1_comp) + cell_data(i,j,k-1,RhoQ2_comp);
                    if ( (qt_lo > qt_i) && (qt_hi < qt_i) ) {
                        zi   = myhalf * (z_cc_arr(i,j,k) + z_cc_arr(i,j,k-1));
                        rhoi = myhalf * (cell_data(i,j,k,Rho_comp) + cell_data(i,j,k-1,Rho_comp));
                    }
                }
 
                // Decompose the integral to get the fluxes at w-faces
                Real q_int_inf = q_int[khi+1];
                for (int k(klo); k<=khi+1; ++k) {
                    int lk       = k - klo;
                    Real z       = myhalf * (z_cc_arr(i,j,k) + z_cc_arr(i,j,k-1));
                    rad_flux[lk] = F1*std::exp(-q_int[lk]) + F0*std::exp(-(q_int_inf - q_int[lk]));
                    if (z > zi) {
                      rad_flux[lk] += rhoi * Cp_d * D * ( std::pow(z-zi,Real(4.)/three)/Real(4.) + zi*std::pow(z-zi,one/three) ) ;
                    }
                }
 
                // Compute the radiative heating source
                for (int k(klo); k<=khi; ++k) {
                    int lk       = k - klo;
                    // Average to w-faces when looping CC
                    Real dzInv   = (z_cc_arr) ? one/ (myhalf * (z_cc_arr(i,j,k+1) - z_cc_arr(i,j,k-1))) : dxInv[2];
                    // NOTE: Fnet  = Up - Dn (all fluxes are up here)
                    //       dT/dt = dF/dz * (1/(-rho*Cp))
                    Real dTdt    = (rad_flux[lk+1] - rad_flux[lk]) * dzInv / (-cell_data(i,j,k,Rho_comp)*Cp_d);
                    Real qv      = cell_data(i,j,k,RhoQ1_comp)/cell_data(i,j,k,Rho_comp);
                    Real iexner  = one/getExnergivenRTh(cell_data(i,j,k,RhoTheta_comp), R_d/Cp_d, qv);
                    // Convert dT/dt to dTheta/dt and multiply rho
                    cell_src(i,j,k,RhoTheta_comp) += cell_data(i,j,k,Rho_comp) * dTdt * iexner;
                }
            });
        }
    } // mfi
    } // OMP
}

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