ERF_ComputeDiffusivityMYNN25.cpp File Reference

#include "ERF_SurfaceLayer.H"
#include "ERF_DirectionSelector.H"
#include "ERF_Diffusion.H"
#include "ERF_Constants.H"
#include "ERF_TurbStruct.H"
#include "ERF_PBLModels.H"

Include dependency graph for ERF_ComputeDiffusivityMYNN25.cpp:

Macros
#define	EXTRA_MYNN25_CHECKS   0

Functions
void	ComputeDiffusivityMYNN25 (const MultiFab &xvel, const MultiFab &yvel, const MultiFab &cons_in, MultiFab &eddyViscosity, const Geometry &geom, const TurbChoice &turbChoice, std::unique_ptr< SurfaceLayer > &SurfLayer, bool use_terrain_fitted_coords, bool use_moisture, int level, const BCRec *bc_ptr, bool, const std::unique_ptr< MultiFab > &z_phys_nd, const std::unique_ptr< MultiFab > &z_phys_cc, const MoistureComponentIndices &moisture_indices)

Macro Definition Documentation

EXTRA_MYNN25_CHECKS

#define EXTRA_MYNN25_CHECKS   0

Function Documentation

ComputeDiffusivityMYNN25()

void ComputeDiffusivityMYNN25	(	const MultiFab &	xvel,
		const MultiFab &	yvel,
		const MultiFab &	cons_in,
		MultiFab &	eddyViscosity,
		const Geometry &	geom,
		const TurbChoice &	turbChoice,
		std::unique_ptr< SurfaceLayer > &	SurfLayer,
		bool	use_terrain_fitted_coords,
		bool	use_moisture,
		int	level,
		const BCRec *	bc_ptr,
		bool	,
		const std::unique_ptr< MultiFab > &	z_phys_nd,
		const std::unique_ptr< MultiFab > &	z_phys_cc,
		const MoistureComponentIndices &	moisture_indices
	)

{
    auto mynn     = turbChoice.pbl_mynn;
    auto level2   = turbChoice.pbl_mynn_level2;
 
    Real Lt_alpha = (mynn.config == MYNNConfigType::CHEN2021) ? Real(0.1) : Real(0.23);
 
    // Dirichlet flags to switch derivative stencil
    bool c_ext_dir_on_zlo = ( (bc_ptr[BCVars::cons_bc].lo(2) == ERFBCType::ext_dir) );
    bool c_ext_dir_on_zhi = ( (bc_ptr[BCVars::cons_bc].hi(2) == ERFBCType::ext_dir) );
    bool u_ext_dir_on_zlo = ( (bc_ptr[BCVars::xvel_bc].lo(2) == ERFBCType::ext_dir) );
    bool u_ext_dir_on_zhi = ( (bc_ptr[BCVars::xvel_bc].hi(2) == ERFBCType::ext_dir) );
    bool v_ext_dir_on_zlo = ( (bc_ptr[BCVars::yvel_bc].lo(2) == ERFBCType::ext_dir) );
    bool v_ext_dir_on_zhi = ( (bc_ptr[BCVars::yvel_bc].hi(2) == ERFBCType::ext_dir) );
 
    // Epsilon
    Real eps = std::numeric_limits<Real>::epsilon();
 
#ifdef _OPENMP
#pragma omp parallel if (Gpu::notInLaunchRegion())
#endif
    for ( MFIter mfi(eddyViscosity,false); mfi.isValid(); ++mfi) {
 
        const Box &bx = mfi.growntilebox(1);
        const Array4<Real const>& cell_data = cons_in.array(mfi);
        const Array4<Real      >& K_turb    = eddyViscosity.array(mfi);
        const Array4<Real const>& uvel      = xvel.array(mfi);
        const Array4<Real const>& vvel      = yvel.array(mfi);
 
        // Compute some quantities that are constant in each column
        // Sbox is shrunk to only include the interior of the domain in the vertical direction to compute integrals
        // Box includes one ghost cell in each direction
        const Box &dbx = geom.Domain();
        Box sbx(bx.smallEnd(), bx.bigEnd());
        sbx.grow(2,-1);
        AMREX_ALWAYS_ASSERT(sbx.smallEnd(2) == dbx.smallEnd(2) && sbx.bigEnd(2) == dbx.bigEnd(2));
 
        const GeometryData gdata = geom.data();
 
        const Box xybx = PerpendicularBox<ZDir>(bx, IntVect{0,0,0});
        FArrayBox qturb(bx,1);
        FArrayBox qintegral(xybx,2);
        qintegral.setVal<RunOn::Device>(0);
        const Array4<Real> qint = qintegral.array();
        const Array4<Real> qvel = qturb.array();
 
        // vertical integrals to compute lengthscale
        if (use_terrain_fitted_coords) {
            const Array4<Real const> &z_nd_arr = z_phys_nd->array(mfi);
            const auto invCellSize = geom.InvCellSizeArray();
            ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
            {
                // q^2 / 2 is the TKE
                qvel(i,j,k) = std::sqrt(two * cell_data(i,j,k,RhoKE_comp) / cell_data(i,j,k,Rho_comp));
                AMREX_ALWAYS_ASSERT_WITH_MESSAGE(qvel(i,j,k) > zero, "KE must have a positive value");
 
                Real fac = (sbx.contains(i,j,k)) ? one : zero;
                const Real Zval = Compute_Zrel_AtCellCenter(i,j,k,z_nd_arr);
                const Real dz   = Compute_h_zeta_AtCellCenter(i,j,k,invCellSize,z_nd_arr);
                Gpu::Atomic::Add(&qint(i,j,0,0), Zval*qvel(i,j,k)*dz*fac);
                Gpu::Atomic::Add(&qint(i,j,0,1),      qvel(i,j,k)*dz*fac);
            });
        } else {
            ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
            {
                // q^2 / 2 is the TKE
                qvel(i,j,k) = std::sqrt(two * cell_data(i,j,k,RhoKE_comp) / cell_data(i,j,k,Rho_comp));
                AMREX_ALWAYS_ASSERT_WITH_MESSAGE(qvel(i,j,k) > zero, "KE must have a positive value");
 
                // Not multiplying by dz: it's constant and would fall out when we divide qint0/qint1 anyway
 
                Real fac = (sbx.contains(i,j,k)) ? one : zero;
                const Real Zval = gdata.ProbLo(2) + (k + myhalf)*gdata.CellSize(2);
                Gpu::Atomic::Add(&qint(i,j,0,0), Zval*qvel(i,j,k)*fac);
                Gpu::Atomic::Add(&qint(i,j,0,1),      qvel(i,j,k)*fac);
            });
        }
 
        int izmin = geom.Domain().smallEnd(2);
        int izmax = geom.Domain().bigEnd(2);
 
        // Spatially varying MOST
        Real d_kappa   = KAPPA;
        Real d_gravity = CONST_GRAV;
 
        const auto& t_mean_mf = SurfLayer->get_mac_avg(level,4); // theta_v
        const auto& q_mean_mf = SurfLayer->get_mac_avg(level,3); // q_v
        const auto& u_star_mf = SurfLayer->get_u_star(level);
        const auto& t_star_mf = SurfLayer->get_t_star(level);
        const auto& q_star_mf = SurfLayer->get_q_star(level);
 
        const auto& tm_arr     = t_mean_mf->const_array(mfi);
        const auto& qm_arr     = q_mean_mf->const_array(mfi);
        const auto& u_star_arr = u_star_mf->const_array(mfi);
        const auto& t_star_arr = t_star_mf->const_array(mfi);
        const auto& q_star_arr = (use_moisture) ? q_star_mf->const_array(mfi) : Array4<Real>{};
 
        const Array4<Real const> z_nd_arr = z_phys_nd->const_array(mfi);
        const PBLDerivativeDzInv_T pbl_derivative_dz_inv{z_phys_cc->const_array(mfi)};
 
        ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k) noexcept
        {
            // Compute some partial derivatives that we will need (second order)
            // U and V derivatives are interpolated to account for staggered grid
            Real dthetavdz, dudz, dvdz;
            ComputeVerticalDerivativesPBL(i, j, k,
                                          uvel, vvel, cell_data, izmin, izmax, pbl_derivative_dz_inv(i,j,k),
                                          c_ext_dir_on_zlo, c_ext_dir_on_zhi,
                                          u_ext_dir_on_zlo, u_ext_dir_on_zhi,
                                          v_ext_dir_on_zlo, v_ext_dir_on_zhi,
                                          dthetavdz, dudz, dvdz,
                                          moisture_indices);
 
            // Spatially varying MOST
            Real theta0 = tm_arr(i,j,0);
            Real qv0    = qm_arr(i,j,0);
            Real surface_heat_flux = -u_star_arr(i,j,0) * t_star_arr(i,j,0);
            Real surface_latent_heat{0};
            if (use_moisture) {
                // Compute buoyancy flux (Stull Eqn. 4.4.5d)
                surface_latent_heat = -u_star_arr(i,j,0) * q_star_arr(i,j,0);
                surface_heat_flux *= (one + Real(0.61)*qv0);
                surface_heat_flux += Real(0.61) * theta0 * surface_latent_heat;
            }
 
            Real l_obukhov;
            if (std::abs(surface_heat_flux) > eps) {
                l_obukhov = -( theta0 * u_star_arr(i,j,0)*u_star_arr(i,j,0)*u_star_arr(i,j,0) )
                           / ( d_kappa * d_gravity * surface_heat_flux );
            } else {
                l_obukhov = std::numeric_limits<Real>::max();
            }
 
            // Surface-layer length scale (NN09, Eqn. 53)
            AMREX_ASSERT(l_obukhov != 0);
            int lk = amrex::max(k,0);
            const Real zval = use_terrain_fitted_coords ? Compute_Zrel_AtCellCenter(i,j,lk,z_nd_arr)
                                          : gdata.ProbLo(2) + (lk + myhalf)*gdata.CellSize(2);
            const Real zeta = zval/l_obukhov;
            Real l_S;
            if (zeta >= one) {
                l_S = KAPPA*zval/Real(3.7);
            } else if (zeta >= 0) {
                l_S = KAPPA*zval/(1+Real(2.7)*zeta);
            } else {
                l_S = KAPPA*zval*std::pow(one - Real(100.0) * zeta, Real(0.2));
            }
 
            // ABL-depth length scale (NN09, Eqn. 54)
            Real l_T;
            if (qint(i,j,0,1) > zero) {
                l_T = Lt_alpha*qint(i,j,0,0)/qint(i,j,0,1);
            } else {
                l_T = std::numeric_limits<Real>::max();
            }
 
            // Buoyancy length scale (NN09, Eqn. 55)
            Real l_B;
            if (dthetavdz > 0) {
                Real N_brunt_vaisala = std::sqrt(CONST_GRAV/theta0 * dthetavdz);
                if (zeta < 0) {
                    Real qc = CONST_GRAV/theta0 * surface_heat_flux * l_T; // velocity scale
                    qc = std::pow(qc,one/three);
                    l_B = (one + Real(5.0)*std::sqrt(qc/(N_brunt_vaisala * l_T))) * qvel(i,j,k)/N_brunt_vaisala;
                } else {
                    l_B = qvel(i,j,k) / N_brunt_vaisala;
                }
            } else {
                l_B = std::numeric_limits<Real>::max();
            }
 
            // Master length scale
            Real Lm;
            if (mynn.config == MYNNConfigType::CHEN2021) {
                Lm = std::pow(one/(l_S*l_S) + one/(l_T*l_T) + one/(l_B*l_B), -myhalf);
            } else {
                // NN09, Eqn 52
                Lm = one / (one/l_S + one/l_T + one/l_B);
            }
 
            // Calculate nondimensional production terms
            Real shearProd  = dudz*dudz + dvdz*dvdz;
            Real buoyProd   = -(CONST_GRAV/theta0) * dthetavdz;
            Real L2_over_q2 = Lm*Lm/(qvel(i,j,k)*qvel(i,j,k));
            Real GM         = L2_over_q2 * shearProd;
            Real GH         = L2_over_q2 * buoyProd;
 
            // Equilibrium (Level-2) q calculation follows NN09, Appendix A
            Real Rf  = level2.calc_Rf(GM, GH);
            Real SM2 = level2.calc_SM(Rf);
            Real qe2 = mynn.B1 * Lm*Lm * SM2 * (one-Rf) * shearProd;
            Real qe  = (qe2 < zero) ? zero : std::sqrt(qe2);
 
            // Level 2 limiting introduced by Helfand and Labraga 1988 (NN09, Eqn. 42)
            Real alphac  = (qvel(i,j,k) >= qe) ? one : qvel(i,j,k) / (qe + eps);
//#if EXTRA_MYNN25_CHECKS
#if 0
            // VERY verbose diagnostic
            Real Ri = -GH/(GM+level2.eps);
            if (alphac < 1) {
                AllPrint() << "Level 2 limiter at " << IntVect(i,j,k) << " :"
                    << " ustar= " << u_star_arr(i,j,0)
                    << " alphac= " << alphac
                    << " Ri,SM2,SH2= " << Ri << " " << SM2 << " " << level2.calc_SH(Rf)
                    << std::endl;
            }
#endif
 
            // Level Real(2.5) stability functions
            Real SM, SH, SQ;
            mynn.calc_stability_funcs(SM,SH,SQ,GM,GH,alphac);
 
            // Clip SM, SH following WRF
            SM = amrex::min(amrex::max(SM, mynn.SMmin), mynn.SMmax);
            SH = amrex::min(amrex::max(SH, mynn.SHmin), mynn.SHmax);
#if EXTRA_MYNN25_CHECKS
            if (SM == mynn.SMmin) {
                Warning("SM clipped at min val");
            } else if (SM == mynn.SMmax) {
                Warning("SM clipped at max val");
            }
            if (SH == mynn.SHmin) {
                Warning("SH clipped at min val");
            } else if (SH == mynn.SHmax) {
                Warning("SH clipped at max val");
            }
#endif
 
            // Finally, compute the eddy viscosity/diffusivities
            const Real rho = cell_data(i,j,k,Rho_comp);
            K_turb(i,j,k,EddyDiff::Mom_v)   = rho * Lm * qvel(i,j,k) * SM;
            K_turb(i,j,k,EddyDiff::Theta_v) = rho * Lm * qvel(i,j,k) * SH;
            K_turb(i,j,k,EddyDiff::KE_v)    = rho * Lm * qvel(i,j,k) * SQ;
 
            // TODO: implement partial-condensation scheme?
            // Currently, implementation matches NN09 without rain (i.e.,
            // the liquid water potential temperature is equal to the
            // potential temperature.
 
            // NN09 gives the total water content flux; this assumes that
            // all the species have the same eddy diffusivity
            if (mynn.diffuse_moistvars) {
                K_turb(i,j,k,EddyDiff::Q_v) = rho * Lm * qvel(i,j,k) * SH;
            }
 
            K_turb(i,j,k,EddyDiff::Turb_lengthscale) = Lm;
        });
    }
}

Referenced by ComputeTurbulentViscosity().

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