ERF_SurfaceLayer.H

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#ifndef ERF_SURFACELAYER_H
#define ERF_SURFACELAYER_H
 
#include "AMReX_Geometry.H"
#include "AMReX_ParmParse.H"
#include "AMReX_FArrayBox.H"
#include "AMReX_MultiFab.H"
#include "AMReX_iMultiFab.H"
#include "AMReX_MFInterpolater.H"
 
#include "ERF_IndexDefines.H"
#include "ERF_Constants.H"
#include "ERF_MOSTAverage.H"
#include "ERF_MOSTStress.H"
#include "ERF_EBMOSTStress.H"
#include "ERF_SurfaceDiagnosticSource.H"
#include "ERF_TerrainMetrics.H"
#include "ERF_PBLHeight.H"
#include "ERF_MicrophysicsUtils.H"
#include "ERF_EB.H"
 
/** Abstraction layer for different surface layer schemes (e.g. MOST, Cd)
 *
 * van der Laan, P., Kelly, M. C., & Sørensen, N. N. (2017). A new k-epsilon
 * model consistent with Monin-Obukhov similarity theory. Wind Energy,
 * 20(3), 479–amrex::Real(489.) https://doi.org/amrex::Real(10.1002)/we.2017
 *
 * Consistent with Dyer (1974) formulation from page 57, Chapter 2, Modeling
 * the vertical ABL structure in Modelling of Atmospheric Flow Fields,
 * Demetri P Lalas and Corrado F Ratto, January 1996,
 * https://doi.org/amrex::Real(10.1142)/amrex::Real(2975.)
 */
class SurfaceLayer
{
 
public:
  /**
   * Construct the surface-layer interface.
   *
   * @param[in]     geom                geometry for all AMR levels
   * @param[in,out] use_rot_surface_flux whether to use rotated surface fluxes
   * @param[in]     a_pp_prefix         ParmParse prefix used by MOST averages
   * @param[in]     Qv_prim             primitive water-vapor fields by level
   * @param[in]     z_phys_nd           nodal physical-height fields by level
   * @param[in]     a_mesh_type         mesh type
   * @param[in]     a_terrain_type      terrain representation
   * @param[in]     a_turb_choice       turbulence-model options
   * @param[in]     start_low_time      first available low-boundary-data time
   * @param[in]     final_low_time      final available low-boundary-data time
   * @param[in]     low_time_interval   low-boundary-data time interval
   * @param[in]     eb_vec              optional embedded-boundary geometry data
   */
  explicit SurfaceLayer (const amrex::Vector<amrex::Geometry>& geom,
                         bool& use_rot_surface_flux,
                         std::string a_pp_prefix,
                         amrex::Vector<std::unique_ptr<amrex::MultiFab>>& Qv_prim,
                         amrex::Vector<std::unique_ptr<amrex::MultiFab>>& z_phys_nd,
                         const MeshType& a_mesh_type,
                         const TerrainType& a_terrain_type,
                         const TurbChoice& a_turb_choice,
                         double start_low_time,
                         double final_low_time,
                         double low_time_interval = 0.0,
                         const amrex::Vector<const eb_*>& eb_vec = {})
  : m_geom(geom),
    m_rotate(use_rot_surface_flux),
    m_start_low_time(start_low_time),
    m_final_low_time(final_low_time),
    m_low_time_interval(low_time_interval),
    m_eb_vec(eb_vec),
    m_terrain_type(a_terrain_type),
    m_ma(geom, (z_phys_nd[0] != nullptr), a_pp_prefix, a_mesh_type, a_terrain_type, eb_vec)
  {
      // We have a moisture model if Qv_prim is a valid pointer
      use_moisture = (Qv_prim[0].get());
 
      // Get roughness
      amrex::ParmParse pp("erf");
      pp.query("most.z0", z0_const);
 
      // Specify how to compute the flux
      if (use_rot_surface_flux) {
          flux_type = FluxCalcType::ROTATE;
      } else {
          std::string flux_string_in;
          std::string flux_string{"moeng"};
          auto read_flux = pp.query("surface_layer.flux_type", flux_string_in);
          if (read_flux) {
              flux_string = amrex::toLower(flux_string_in);
          }
          if (flux_string == "donelan") {
              flux_type = FluxCalcType::DONELAN;
          } else if (flux_string == "moeng") {
              flux_type = FluxCalcType::MOENG;
          } else if (flux_string == "rico") {
                flux_type = FluxCalcType::RICO;
          } else if (flux_string == "bulk_coeff") {
              flux_type = FluxCalcType::BULK_COEFF;
          } else if (flux_string == "custom") {
              flux_type = FluxCalcType::CUSTOM;
          } else {
              amrex::Abort("Undefined MOST flux type!");
          }
      }
 
      // Include w* to handle free convection (Beljaars 1995, QJRMS)
      pp.query("most.include_wstar", m_include_wstar);
 
      std::string pblh_string_in;
      std::string pblh_string{"none"};
      auto read_pblh = pp.query("most.pblh_calc", pblh_string_in);
      if (read_pblh) {
          pblh_string = amrex::toLower(pblh_string_in);
      }
      if (pblh_string == "none") {
          pblh_type = PBLHeightCalcType::None;
      } else if (pblh_string == "mynn25") {
          pblh_type = PBLHeightCalcType::MYNN25;
      } else if (pblh_string == "mynnedmf") {
          pblh_type = PBLHeightCalcType::MYNN25;
      } else if (pblh_string == "ysu") {
          pblh_type = PBLHeightCalcType::YSU;
      } else if (pblh_string == "mrf") {
          pblh_type = PBLHeightCalcType::MRF;
      } else {
          amrex::Abort("Undefined PBLH calc type!");
      }
 
      // Get surface temperature
      auto erf_st = pp.query("most.surf_temp", surf_temp);
      if (erf_st) { default_land_surf_temp  = surf_temp; }
 
      // Get surface moisture
      bool erf_sq = false;
      if (use_moisture) { erf_sq = pp.query("most.surf_moist", surf_moist); }
      if (erf_sq) { default_land_surf_moist = surf_moist; }
 
      // Custom type user must specify the fluxes
      if (flux_type == FluxCalcType::CUSTOM ||
          flux_type == FluxCalcType::RICO) {
          theta_type = ThetaCalcType::HEAT_FLUX;
          moist_type = MoistCalcType::MOISTURE_FLUX;
          pp.get("most.ustar", custom_ustar);
          pp.get("most.tstar", custom_tstar);
          pp.get("most.qstar", custom_qstar);
          pp.query("most.rhosurf", custom_rhosurf);
          if (custom_qstar != 0) {
              AMREX_ASSERT_WITH_MESSAGE(use_moisture,
              "Specified custom MOST qv flux without moisture model!");
          }
          amrex::Print() << "Using specified ustar, tstar, qstar for MOST = "
                         << custom_ustar << " " << custom_tstar << " "
                         << custom_qstar << std::endl;
 
      // Bulk transfer coefficient (must specify coeffs and surface values)
      } else if (flux_type == FluxCalcType::BULK_COEFF) {
          pp.get("most.Cd", m_Cd);
          pp.get("most.Ch", m_Ch);
          pp.get("most.Cq", m_Cq);
          pp.get("most.surf_temp", default_land_surf_temp);
          pp.get("most.surf_moist", default_land_surf_moist);
          amrex::Print() << "Using specified Cd, Ch, Cq for MOST = "
                         << m_Cd << " " << m_Ch << " "
                         << m_Cq << std::endl;
 
      // Specify surface temperature/moisture or surface flux
      } else {
          if (erf_st) {
              theta_type = ThetaCalcType::SURFACE_TEMPERATURE;
              pp.query("most.surf_heating_rate", surf_heating_rate); // [K/h]
 
              // Modify rate to be in units of K / s rather than K / hr
              surf_heating_rate /= amrex::Real(3600.0);        // [K/s]
 
              if (pp.query("most.surf_temp_flux", surf_temp_flux)) {
                  amrex::Abort("Can only specify one of surf_temp_flux or surf_heating_rate");
              }
          } else {
              pp.query("most.surf_temp_flux", surf_temp_flux);
 
              if (pp.query("most.surf_heating_rate", surf_heating_rate)) {
                  amrex::Abort("Can only specify one of surf_temp_flux or surf_heating_rate");
              }
              if (std::abs(surf_temp_flux) >
                  std::numeric_limits<amrex::Real>::epsilon()) {
                  theta_type = ThetaCalcType::HEAT_FLUX;
              } else {
                  theta_type = ThetaCalcType::ADIABATIC;
              }
          }
 
          if (erf_sq) {
              moist_type = MoistCalcType::SURFACE_MOISTURE;
          } else {
              pp.query("most.surf_moist_flux", surf_moist_flux);
              if (std::abs(surf_moist_flux) >
                  std::numeric_limits<amrex::Real>::epsilon()) {
                  moist_type = MoistCalcType::MOISTURE_FLUX;
              } else {
                  moist_type = MoistCalcType::ADIABATIC;
              }
          }
      }
 
      if (flux_type == FluxCalcType::RICO)
      {
          pp.query("most.rico.theta_z0", rico_theta_z0);
          pp.query("most.rico.qsat_z0", rico_qsat_z0);
      }
 
      // Make sure the inputs file doesn't try to use most.roughness_type
      std::string bogus_input;
      if (pp.query("most.roughness_type", bogus_input) > 0) {
          amrex::Abort("most.roughness_type is deprecated; use "
                       "most.roughness_type_land and/or most.roughness_type_sea");
      }
 
      // Specify how to compute the surface flux over land (if there is any)
      std::string rough_land_string_in;
      std::string rough_land_string{"constant"};
      auto read_rough_land =
          pp.query("most.roughness_type_land", rough_land_string_in);
      if (read_rough_land) {
          rough_land_string = amrex::toLower(rough_land_string_in);
      }
      if (rough_land_string == "constant") {
          rough_type_land = RoughCalcType::CONSTANT;
      } else {
          amrex::Abort("Undefined MOST roughness type for land!");
      }
 
      // Specify how to compute the surface flux over sea (if there is any)
      std::string rough_sea_string_in;
      std::string rough_sea_string{"charnock"};
      auto read_rough_sea = pp.query("most.roughness_type_sea", rough_sea_string_in);
      if (read_rough_sea) {
          rough_sea_string = amrex::toLower(rough_sea_string_in);
      }
      if (rough_sea_string == "charnock") {
          rough_type_sea = RoughCalcType::CHARNOCK;
          pp.query("most.charnock_constant", cnk_a);
          pp.query("most.charnock_viscosity", cnk_visc);
          if (cnk_a > 0) {
              amrex::Print() << "If there is water, Charnock relation with C_a="
                             << cnk_a << (cnk_visc ? " and viscosity" : "")
                             << " will be used" << std::endl;
          } else {
              amrex::Print() << "If there is water, Charnock relation with variable "
                  "Charnock parameter (COARE3.0)"
                             << (cnk_visc ? " and viscosity" : "") << " will be used"
                             << std::endl;
          }
      } else if (rough_sea_string == "coare3.0") {
          rough_type_sea = RoughCalcType::CHARNOCK;
          amrex::Print() << "If there is water, Charnock relation with variable "
              "Charnock parameter (COARE3.0)"
                         << (cnk_visc ? " and viscosity" : "") << " will be used"
                         << std::endl;
          cnk_a = -1;
      } else if (rough_sea_string == "donelan") {
          rough_type_sea = RoughCalcType::DONELAN;
      } else if (rough_sea_string == "modified_charnock") {
          rough_type_sea = RoughCalcType::MODIFIED_CHARNOCK;
          pp.query("most.modified_charnock_depth", depth);
      } else if (rough_sea_string == "wave_coupled") {
          rough_type_sea = RoughCalcType::WAVE_COUPLED;
      } else if (rough_sea_string == "constant") {
          rough_type_sea = RoughCalcType::CONSTANT;
      } else {
          amrex::Abort("Undefined MOST roughness type for sea!");
      }
 
      // use skin temperature instead of sea-surface temperature
      // (wrfinput data may have lower resolution SST data)
      pp.query("most.ignore_sst", m_ignore_sst);
 
      // If we're using the RANS k model, then we need to update the dirichlet
      // BC based on the instantaneous u* and θ*; the turbulence modeling
      // choices can vary per level but for now, assume that if specified then
      // all levels are using the same RANS model.
      m_update_k_rans = (a_turb_choice.rans_type == RANSType::kEqn &&
                         a_turb_choice.dirichlet_k == true);
      if (m_update_k_rans) {
          inv_Cmu2 = one / (a_turb_choice.Cmu0 * a_turb_choice.Cmu0);
          theta_ref = a_turb_choice.theta_ref;
      }
 
  } // constructor
 
  /**
   * Allocate and initialize surface-layer data for one AMR level.
   *
   * @param[in]     lev           level index
   * @param[in]     nlevs         number of AMR levels
   * @param[in]     mfv           conserved and velocity MultiFabs for this level
   * @param[in]     Theta_prim    primitive potential-temperature field
   * @param[in]     Qv_prim       primitive water-vapor field
   * @param[in]     Qr_prim       primitive rain-water field
   * @param[in]     z_phys_nd     nodal physical-height field
   * @param[in]     Hwave         wave-height field
   * @param[in]     Lwave         wavelength field
   * @param[in]     eddyDiffs     eddy-diffusivity field
   * @param[in]     lsm_data      land-surface-model data fields
   * @param[in]     lsm_data_name names for lsm_data entries
   * @param[in]     lsm_flux      land-surface-model flux fields
   * @param[in]     lsm_flux_name names for lsm_flux entries
   * @param[in]     sst_lev       sea-surface-temperature data by time
   * @param[in]     tsk_lev       skin-temperature data by time
   * @param[in]     lmask_lev     land-mask data by time
   */
  void make_SurfaceLayer_at_level (const int& lev,
                                   int nlevs,
                                   const amrex::Vector<amrex::MultiFab*>& mfv,
                                   std::unique_ptr<amrex::MultiFab>& Theta_prim,
                                   std::unique_ptr<amrex::MultiFab>& Qv_prim,
                                   std::unique_ptr<amrex::MultiFab>& Qr_prim,
                                   std::unique_ptr<amrex::MultiFab>& z_phys_nd,
                                   amrex::MultiFab* Hwave,
                                   amrex::MultiFab* Lwave,
                                   amrex::MultiFab* eddyDiffs,
                                   amrex::Vector<amrex::MultiFab*> lsm_data,
                                   amrex::Vector<std::string>      lsm_data_name,
                                   amrex::Vector<amrex::MultiFab*> lsm_flux,
                                   amrex::Vector<std::string>      lsm_flux_name,
                                   amrex::Vector<std::unique_ptr<amrex::MultiFab>>& sst_lev,
                                   amrex::Vector<std::unique_ptr<amrex::MultiFab>>& tsk_lev,
                                   amrex::Vector<std::unique_ptr<amrex::iMultiFab>>& lmask_lev)
  {
      // Update MOST Average
      m_ma.make_MOSTAverage_at_level(lev, mfv,
                                     Theta_prim, Qv_prim, Qr_prim,
                                     z_phys_nd);
 
      // Get CC vars
      amrex::MultiFab& mf = *(mfv[0]);
 
      amrex::ParmParse pp("erf");
 
      // Do we have a time-varying surface roughness that needs to be saved?
      if (lev == 0) {
          const int nghost = 0; // ghost cells not included
          int lmask_min = lmask_min_reduce(*lmask_lev[0].get(), nghost);
          amrex::ParallelDescriptor::ReduceIntMin(lmask_min);
 
          m_var_z0 = (lmask_min < 1) & (rough_type_sea != RoughCalcType::CONSTANT);
          if (m_var_z0) {
              std::string rough_sea_string{"charnock"};
              pp.query("most.roughness_type_sea", rough_sea_string);
              amrex::Print() << "Variable sea roughness (type " << rough_sea_string
                             << ")" << std::endl;
          }
      }
 
      if (m_eddyDiffs_lev.size() < lev+1) {
          m_Hwave_lev.resize(nlevs);
          m_Lwave_lev.resize(nlevs);
          m_eddyDiffs_lev.resize(nlevs);
 
          m_lsm_data_lev.resize(nlevs);
          m_lsm_flux_lev.resize(nlevs);
 
          m_sst_lev.resize(nlevs);
          m_tsk_lev.resize(nlevs);
          m_lmask_lev.resize(nlevs);
 
          // Size the MOST params for all levels
          z_0.resize(nlevs);
          u_star.resize(nlevs);
          w_star.resize(nlevs);
          t_star.resize(nlevs);
          q_star.resize(nlevs);
          t_surf.resize(nlevs);
          q_surf.resize(nlevs);
          surface_diagnostic_source.resize(nlevs);
          olen.resize(nlevs);
          pblh.resize(nlevs);
      }
 
      // Get pointers to SST,TSK and LANDMASK data
      int nt_tot_sst = sst_lev.size();
      m_sst_lev[lev].resize(nt_tot_sst);
      for (int nt(0); nt < nt_tot_sst; ++nt) {
          m_sst_lev[lev][nt] = sst_lev[nt].get();
      }
      int nt_tot_tsk = static_cast<int>(tsk_lev.size());
      m_tsk_lev[lev].resize(nt_tot_tsk);
      for (int nt(0); nt < nt_tot_tsk; ++nt) {
          m_tsk_lev[lev][nt] = tsk_lev[nt].get();
      }
      int nt_tot_lmask = static_cast<int>(lmask_lev.size());
      m_lmask_lev[lev].resize(nt_tot_lmask);
      for (int nt(0); nt < nt_tot_lmask; ++nt) {
          m_lmask_lev[lev][nt] = lmask_lev[nt].get();
      }
 
      // Get pointers to wave data
      m_Hwave_lev[lev] = Hwave;
      m_Lwave_lev[lev] = Lwave;
      m_eddyDiffs_lev[lev] = eddyDiffs;
 
      // Get pointers to LSM data and Fluxes
      int ndata = static_cast<int>(lsm_data.size());
      int nflux = static_cast<int>(lsm_flux.size());
      m_lsm_data_name.resize(ndata);
      m_lsm_data_lev[lev].resize(ndata);
      m_lsm_flux_name.resize(nflux);
      m_lsm_flux_lev[lev].resize(nflux);
      for (int n(0); n < ndata; ++n) {
          m_lsm_data_name[n]     = lsm_data_name[n];
          m_lsm_data_lev[lev][n] = lsm_data[n];
          const std::string lc_name = amrex::toLower(lsm_data_name[n]);
          if (lc_name == "theta" || lc_name == "t_surf") {
              m_has_lsm_tsurf  = true;
              m_lsm_tsurf_indx = n;
              m_has_ocean_lsm_tsurf = (lc_name == "t_surf");
          }
      }
      int n_valid_lsm_flux = 0;
      bool has_soil_t_flux = false;
      for (int n(0); n < nflux; ++n) {
          m_lsm_flux_name[n]     = lsm_flux_name[n];
          m_lsm_flux_lev[lev][n] = lsm_flux[n];
          if (m_lsm_flux_lev[lev][n]) { ++n_valid_lsm_flux; }
          if (amrex::toLower(m_lsm_flux_name[n]) == "soil_t_flux") {
              has_soil_t_flux = true;
          }
      }
      AMREX_ALWAYS_ASSERT((n_valid_lsm_flux==0 || n_valid_lsm_flux>=4 ||
                           (n_valid_lsm_flux==1 && has_soil_t_flux)));
      if (n_valid_lsm_flux>=4) { m_has_lsm_fluxes = true; }
 
      // Check if there is a user-specified roughness file to be read
      std::string fname;
      bool read_z0 = false;
      if ( (flux_type == FluxCalcType::MOENG) ||
           (flux_type == FluxCalcType::ROTATE)) {
          int count = pp.countval("most.roughness_file_name");
          if (count > 1) {
              AMREX_ALWAYS_ASSERT(count >= lev+1);
              pp.query("most.roughness_file_name", fname, lev);
              read_z0 = true;
          } else if (count == 1) {
              if (lev == 0) {
                  pp.query("most.roughness_file_name", fname);
              } else {
                  // we will interpolate from the coarsest level
                  fname = "";
              }
              read_z0 = true;
          }
          // else use z0_const
      }
 
      // Attributes for MFs and FABs
      //--------------------------------------------------------
      // Create a 2D ba for planar terrain, 3D for EB terrain
      amrex::BoxArray ba = mf.boxArray();
      amrex::BoxArray ba_flux;
      amrex::IntVect ng{1,1,0};
 
      if (m_terrain_type == TerrainType::EB) {
          // Use full 3D BoxArray for EB terrain
          ba_flux = ba;
          ng = amrex::IntVect{1,1,1};  // Include z ghost cells
      } else {
          // Collapse to 2D for planar terrain
          amrex::BoxList bl2d = ba.boxList();
          for (auto& b : bl2d) { b.setRange(2,0); }
          ba_flux = amrex::BoxArray(std::move(bl2d));
      }
 
      const amrex::DistributionMapping& dm = mf.DistributionMap();
      const int ncomp = 1;
 
      // Z0 heights FAB
      //--------------------------------------------------------
      z_0[lev].define(ba_flux, dm, ncomp, ng);
      z_0[lev].setVal(z0_const);
      if (read_z0) {
          read_custom_roughness(lev, fname);
      }
 
      // 2D MFs for U*, T*, T_surf
      //--------------------------------------------------------
      u_star[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      u_star[lev]->setVal(bogus_large_value);
 
      w_star[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      w_star[lev]->setVal(bogus_large_value);
 
      t_star[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      t_star[lev]->setVal(zero); // default to neutral
 
      q_star[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      q_star[lev]->setVal(zero); // default to dry
 
      olen[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      olen[lev]->setVal(bogus_large_value);
 
      pblh[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      pblh[lev]->setVal(bogus_large_value);
 
      t_surf[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      t_surf[lev]->setVal(default_land_surf_temp);
 
      q_surf[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      q_surf[lev]->setVal(default_land_surf_moist);
 
      surface_diagnostic_source[lev] = std::make_unique<amrex::MultiFab>(ba_flux, dm, ncomp, ng);
      surface_diagnostic_source[lev]->setVal(
          surface_diagnostics::to_plot_value(surface_diagnostics::SurfaceDiagnosticSource::Missing));
 
      // TODO: Do we want an enum struct for indexing?
 
      bool use_sst = (!m_sst_lev[lev].empty() && m_sst_lev[lev][0]);
      bool use_tsk = (!m_tsk_lev[lev].empty() && m_tsk_lev[lev][0]);
      if (use_sst || use_tsk || m_has_lsm_tsurf) {
          // Valid SST, TSK or LSM data; t_surf set before computing fluxes (avoids
          // extended lambda capture) Note that land temp will be set from m_tsk_lev
          //      while sea temp will be set from m_sst_lev
          theta_type = ThetaCalcType::SURFACE_TEMPERATURE;
 
          // Pathways in fill_tsurf_with_sst_and_tsk
          amrex::Print() << "Using MOST with specified surface temperature ";
          if (m_has_ocean_lsm_tsurf) {
              amrex::Print() << "(OceanSurf: t_surf)" << std::endl;
          } else if (m_has_lsm_tsurf && !use_sst && !use_tsk) {
              amrex::Print() << "(SLM: theta)" << std::endl;
          } else {
              // NOTE: SST from the LOW file populates TSK in update_sst_tsk.
              //       So if we have TSK, it contains everything and has been
              //       sanity checked for valid SST values.
              if (use_tsk) { m_ignore_sst = true; }
              if (use_tsk) {
                  amrex::Print() << "(land: TSK, ";
              } else {
                  amrex::Print() << "(land: T0, ";
              }
              if (use_tsk && !use_sst) {
                  amrex::Print() << "sea: TSK)" << std::endl;
              } else {
                  amrex::Print() << "sea: SST)" << std::endl;
                  AMREX_ALWAYS_ASSERT(m_sst_lev[lev][0]);
              }
          }
      }
  }
 
  /**
   * Update surface fluxes and related surface-layer state.
   *
   * @param[in]     lev                      level index
   * @param[in]     elapsed_time             current elapsed simulation time
   * @param[in]     elapsed_time_since_start_low elapsed time relative to low-data start
   * @param[in,out] cons_in                  conserved state used by the flux update
   * @param[in]     z_phys_nd                nodal physical-height field
   * @param[in]     walldist                 wall-distance field
   * @param[in]     max_iters                maximum MOST iteration count
   */
  void
  update_fluxes (const int& lev,
                 const double& elapsed_time,
                 const double& elapsed_time_since_start_low,
                 amrex::MultiFab& cons_in,
                 const std::unique_ptr<amrex::MultiFab>& z_phys_nd,
                 const std::unique_ptr<amrex::MultiFab>& walldist,
                 int max_iters = 100);
 
  /**
   * Compute MOST fluxes with a selected flux-iteration functor.
   *
   * @param[in]     lev       level index
   * @param[in]     max_iters maximum MOST iteration count
   * @param[in,out] cons_in   conserved state used by the flux computation
   * @param[in]     most_flux flux-iteration functor
   * @param[in]     is_land   whether the land-surface branch is active
   */
  template <typename FluxIter>
  void compute_fluxes (const int& lev,
                       const int& max_iters,
                       amrex::MultiFab& cons_in,
                       const FluxIter& most_flux,
                       bool is_land);
 
  /**
   * Initialize TKE from the current surface friction velocity.
   *
   * @param[in]     lev       level index
   * @param[in,out] cons      conserved state whose TKE component is initialized
   * @param[in]     z_phys_nd nodal physical-height field
   * @param[in]     tkefac    scale factor applied to the initialized TKE
   * @param[in]     zscale    vertical decay scale
   */
  void init_tke_from_ustar (const int& lev,
                            amrex::MultiFab& cons,
                            const std::unique_ptr<amrex::MultiFab>& z_phys_nd,
                            const amrex::Real tkefac = one,
                            const amrex::Real zscale = amrex::Real(700.0));
 
  /**
   * Impose surface-layer boundary conditions for planar terrain.
   *
   * @param[in]     lev        level index
   * @param[in]     mfs        state and velocity fields used by the BC computation
   * @param[in,out] Tau_lev    stress fields to fill
   * @param[in,out] xheat_flux x-face heat flux field
   * @param[in,out] yheat_flux y-face heat flux field
   * @param[in,out] zheat_flux z-face heat flux field
   * @param[in,out] xqv_flux   x-face moisture flux field
   * @param[in,out] yqv_flux   y-face moisture flux field
   * @param[in,out] zqv_flux   z-face moisture flux field
   * @param[in]     z_phys     physical-height field
   */
  void impose_SurfaceLayer_bcs (const int& lev,
                                amrex::Vector<const amrex::MultiFab*> mfs,
                                amrex::Vector<std::unique_ptr<amrex::MultiFab>>& Tau_lev,
                                amrex::MultiFab* xheat_flux,
                                amrex::MultiFab* yheat_flux,
                                amrex::MultiFab* zheat_flux,
                                amrex::MultiFab* xqv_flux,
                                amrex::MultiFab* yqv_flux,
                                amrex::MultiFab* zqv_flux,
                                const amrex::MultiFab* z_phys);
 
  /**
   * Impose surface-layer boundary conditions for embedded-boundary terrain.
   *
   * @param[in]     lev        level index
   * @param[in]     mfs        state and velocity fields used by the BC computation
   * @param[in,out] Tau_lev    EB stress fields to fill
   * @param[in,out] xheat_flux x-face heat flux field
   * @param[in,out] yheat_flux y-face heat flux field
   * @param[in,out] zheat_flux z-face heat flux field
   * @param[in,out] xqv_flux   x-face moisture flux field
   * @param[in,out] yqv_flux   y-face moisture flux field
   * @param[in,out] zqv_flux   z-face moisture flux field
   */
  void impose_SurfaceLayer_bcs_EB (const int& lev,
                                amrex::Vector<const amrex::MultiFab*> mfs,
                                amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>>& Tau_lev,
                                amrex::MultiFab* xheat_flux,
                                amrex::MultiFab* yheat_flux,
                                amrex::MultiFab* zheat_flux,
                                amrex::MultiFab* xqv_flux,
                                amrex::MultiFab* yqv_flux,
                                amrex::MultiFab* zqv_flux);
 
  /**
   * Compute planar-terrain surface-layer flux boundary conditions.
   *
   * @param[in]     lev        level index
   * @param[in]     mfs        state and velocity fields used by the BC computation
   * @param[in,out] Tau_lev    stress fields to fill
   * @param[in,out] xheat_flux x-face heat flux field
   * @param[in,out] yheat_flux y-face heat flux field
   * @param[in,out] zheat_flux z-face heat flux field
   * @param[in,out] xqv_flux   x-face moisture flux field
   * @param[in,out] yqv_flux   y-face moisture flux field
   * @param[in,out] zqv_flux   z-face moisture flux field
   * @param[in]     z_phys     physical-height field
   * @param[in]     flux_comp  flux-computation functor
   */
  template <typename FluxCalc>
  void compute_SurfaceLayer_bcs (const int& lev,
                                 amrex::Vector<const amrex::MultiFab*> mfs,
                                 amrex::Vector<std::unique_ptr<amrex::MultiFab>>& Tau_lev,
                                 amrex::MultiFab* xheat_flux,
                                 amrex::MultiFab* yheat_flux,
                                 amrex::MultiFab* zheat_flux,
                                 amrex::MultiFab* xqv_flux,
                                 amrex::MultiFab* yqv_flux,
                                 amrex::MultiFab* zqv_flux,
                                 const amrex::MultiFab* z_phys,
                                 const FluxCalc& flux_comp);
 
  /**
   * Compute embedded-boundary surface-layer flux boundary conditions.
   *
   * @param[in]     lev        level index
   * @param[in]     mfs        state and velocity fields used by the BC computation
   * @param[in,out] Tau_lev    EB stress fields to fill
   * @param[in,out] xheat_flux x-face heat flux field
   * @param[in,out] yheat_flux y-face heat flux field
   * @param[in,out] zheat_flux z-face heat flux field
   * @param[in,out] xqv_flux   x-face moisture flux field
   * @param[in,out] yqv_flux   y-face moisture flux field
   * @param[in,out] zqv_flux   z-face moisture flux field
   * @param[in]     flux_comp  flux-computation functor
   */
  template <typename FluxCalc>
  void compute_SurfaceLayer_bcs_EB (const int& lev,
                                 amrex::Vector<const amrex::MultiFab*> mfs,
                                 amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>>& Tau_lev,
                                 amrex::MultiFab* xheat_flux,
                                 amrex::MultiFab* yheat_flux,
                                 amrex::MultiFab* zheat_flux,
                                 amrex::MultiFab* xqv_flux,
                                 amrex::MultiFab* yqv_flux,
                                 amrex::MultiFab* zqv_flux,
                                 const FluxCalc& flux_comp);
 
  /**
   * Derive MOST surface parameters from LSM fluxes.
   *
   * @param[in]     lev     level index
   * @param[in,out] cons_in conserved state used by the surface-parameter computation
   */
  void compute_sfc_params_from_lsm_fluxes(const int& lev,
                                          amrex::MultiFab& cons_in);
 
  /**
   * Fill surface temperature from available SST and TSK data.
   *
   * @param[in] lev  level index
   * @param[in] time interpolation time
   */
  void fill_tsurf_with_sst_and_tsk (const int& lev,
                                    const double& time);
 
  /**
   * Fill surface moisture from saturation specific humidity.
   *
   * @param[in] lev       level index
   * @param[in] cons_in   conserved state used to evaluate surface pressure
   * @param[in] z_phys_nd nodal physical-height field
   */
  void fill_qsurf_with_qsat (const int& lev,
                             const amrex::MultiFab& cons_in,
                             const std::unique_ptr<amrex::MultiFab>& z_phys_nd);
 
  /**
   * Fill surface temperature from the LSM surface-temperature field.
   *
   * @param[in] lev level index
   */
  void get_lsm_tsurf (const int& lev);
 
  /**
   * Wrapper around compute_pblh.
   *
   * @param[in]     lev              level index
   * @param[in,out] vars             state variables used by the PBL-height calculation
   * @param[in]     z_phys_cc        cell-centered physical-height field
   * @param[in]     moisture_indices indices for moisture components
   */
  void update_pblh (const int& lev,
                    amrex::Vector<amrex::Vector<amrex::MultiFab>>& vars,
                    amrex::MultiFab* z_phys_cc,
                    const MoistureComponentIndices& moisture_indices);
 
  /**
   * Compute planetary-boundary-layer height with the selected estimator.
   *
   * @param[in]     lev              level index
   * @param[in,out] vars             state variables used by the PBL-height calculation
   * @param[in]     z_phys_cc        cell-centered physical-height field
   * @param[in]     est              PBL-height estimator functor
   * @param[in]     moisture_indice  indices for moisture components
   */
  template <typename PBLHeightEstimator>
  void compute_pblh (const int& lev,
                     amrex::Vector<amrex::Vector<amrex::MultiFab>>& vars,
                     amrex::MultiFab* z_phys_cc,
                     const PBLHeightEstimator& est,
                     const MoistureComponentIndices& moisture_indice);
 
  /**
   * Read custom roughness data for one level.
   *
   * @param[in] lev   level index
   * @param[in] fname roughness-data file name
   */
  void read_custom_roughness (const int& lev,
                              const std::string& fname);
 
  /**
   * Update prescribed surface temperature from the configured heating rate.
   *
   * @param[in] time elapsed simulation time
   */
  void update_surf_temp (const double& time)
  {
      if (m_has_ocean_lsm_tsurf) {
          return;
      }
      if (surf_heating_rate != 0) {
          int nlevs = static_cast<int>(m_geom.size());
          for (int lev = 0; lev < nlevs; lev++) {
              t_surf[lev]->setVal(surf_temp + surf_heating_rate * static_cast<amrex::Real>(time));
              amrex::Print() << "Surface temp at t=" << time << ": "
                             << surf_temp + surf_heating_rate * time << std::endl;
          }
      }
  }
 
  /**
   * Update MOST-average field pointers.
   *
   * @param[in] lev        level index
   * @param[in] vars_old   old-time state variables
   * @param[in] Theta_prim primitive potential-temperature fields by level
   * @param[in] Qv_prim    primitive water-vapor fields by level
   * @param[in] Qr_prim    primitive rain-water fields by level
   */
  void update_mac_ptrs (const int& lev,
                        amrex::Vector<amrex::Vector<amrex::MultiFab>>& vars_old,
                        amrex::Vector<std::unique_ptr<amrex::MultiFab>>& Theta_prim,
                        amrex::Vector<std::unique_ptr<amrex::MultiFab>>& Qv_prim,
                        amrex::Vector<std::unique_ptr<amrex::MultiFab>>& Qr_prim)
  {
      m_ma.update_field_ptrs(lev, vars_old, Theta_prim, Qv_prim, Qr_prim);
  }
 
  /**
   * Return the friction-velocity field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_u_star (const int& lev) { return u_star[lev].get(); }
 
  /**
   * Return the convective velocity scale field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_w_star (const int& lev) { return w_star[lev].get(); }
 
  /**
   * Return the temperature scale field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_t_star (const int& lev) { return t_star[lev].get(); }
 
  /**
   * Return the moisture scale field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_q_star (const int& lev) { return q_star[lev].get(); }
 
  /**
   * Return the Obukhov length field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_olen (const int& lev) { return olen[lev].get(); }
 
  /**
   * Return the planetary-boundary-layer-height field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_pblh (const int& lev) { return pblh[lev].get(); }
 
  /**
   * Return a MOST-average field.
   *
   * @param[in] lev  level index
   * @param[in] comp component index
   */
  const amrex::MultiFab* get_mac_avg (const int& lev, int comp)
  {
      return m_ma.get_average(lev, comp);
  }
 
  /**
   * Return the surface-temperature field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_t_surf (const int& lev) { return t_surf[lev].get(); }
 
  /**
   * Set the surface-temperature field to a constant value.
   *
   * @param[in] lev   level index
   * @param[in] tsurf surface temperature
   */
  void set_t_surf(const int& lev, const amrex::Real tsurf) { t_surf[lev]->setVal(tsurf); }
 
  /**
   * Return the surface-moisture field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_q_surf (const int& lev) { return q_surf[lev].get(); }
 
  /**
   * Set the surface-moisture field to a constant value.
   *
   * @param[in] lev   level index
   * @param[in] qsurf surface moisture
   */
  void set_q_surf(const int& lev, const amrex::Real qsurf) { q_surf[lev]->setVal(qsurf); }
 
  /**
   * Return the surface-diagnostic provenance field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_surface_diagnostic_source (const int& lev) { return surface_diagnostic_source[lev].get(); }
 
  /**
   * Return the minimum reference height for one level.
   *
   * @param[in] lev level index
   */
  amrex::Real get_zref (const int& lev) { return (m_ma.get_zref(lev))->min(0); }
 
  /**
   * Return the roughness-height field.
   *
   * @param[in] lev level index
   */
  amrex::MultiFab* get_z0 (const int& lev) { return &z_0[lev]; }
 
  /**
   * Return whether variable sea roughness is active.
   */
  bool have_variable_sea_roughness () { return m_var_z0; }
 
  /**
   * Return the land-mask field.
   *
   * @param[in] lev level index
   */
  amrex::iMultiFab* get_lmask (const int& lev) { return m_lmask_lev[lev][0]; }
 
  /**
   * Compute the minimum land-mask value over valid and optional ghost cells.
   *
   * @param[in] lmask  land-mask field
   * @param[in] nghost number of ghost cells included in the reduction
   */
  int lmask_min_reduce (amrex::iMultiFab& lmask,
                        const int& nghost)
  {
      int lmask_min = amrex::ReduceMin(lmask, nghost, [=] AMREX_GPU_HOST_DEVICE(
                      amrex::Box const& bx, amrex::Array4<int const> const& lm_arr) -> int
                      {
                          int locmin = std::numeric_limits<int>::max();
                          const auto lo = lbound(bx);
                          const auto hi = ubound(bx);
                          for (int j = lo.y; j <= hi.y; ++j) {
                              for (int i = lo.x; i <= hi.x; ++i) {
                                  locmin = std::min(locmin, lm_arr(i, j, 0));
                              }
                          }
                          return locmin;
                      });
 
      return lmask_min;
  }
 
  /**
   * Update one stored sea-surface-temperature pointer.
   *
   * @param[in] lev     level index
   * @param[in] itime   time-slice index
   * @param[in] sst_ptr sea-surface-temperature field pointer
   */
  void update_sst_ptr(const int lev, const int itime, amrex::MultiFab* sst_ptr) {
      m_sst_lev[lev][itime] = sst_ptr;
  }
 
  /**
   * Update one stored skin-temperature pointer.
   *
   * @param[in] lev     level index
   * @param[in] itime   time-slice index
   * @param[in] tsk_ptr skin-temperature field pointer
   */
  void update_tsk_ptr(const int lev, const int itime, amrex::MultiFab* tsk_ptr) {
      m_tsk_lev[lev][itime] = tsk_ptr;
  }
 
  enum struct FluxCalcType {
    MOENG = 0, ///< Moeng functional form
    DONELAN,   ///< Donelan functional form
    CUSTOM,    ///< Custom constant flux functional form
    BULK_COEFF, ///< Bulk transfer coefficient functional form
    ROTATE,     ///< Terrain rotation flux functional form
    RICO
  };
 
  enum struct ThetaCalcType {
    ADIABATIC = 0,
    HEAT_FLUX,          ///< Heat-flux specified
    SURFACE_TEMPERATURE ///< Surface temperature specified
  };
 
  enum struct MoistCalcType {
    ADIABATIC = 0,
    MOISTURE_FLUX,      ///< Qv-flux specified
    SURFACE_MOISTURE    ///< Surface Qv specified
  };
 
  enum struct RoughCalcType {
    CONSTANT = 0, ///< Constant z0
    CHARNOCK,
    MODIFIED_CHARNOCK,
    DONELAN,
    WAVE_COUPLED
  };
 
  enum struct PBLHeightCalcType { None, MYNN25, YSU, MRF, YSUNew };
 
  FluxCalcType flux_type{FluxCalcType::MOENG};
  ThetaCalcType theta_type{ThetaCalcType::ADIABATIC};
  MoistCalcType moist_type{MoistCalcType::ADIABATIC};
  RoughCalcType rough_type_land{RoughCalcType::CONSTANT};
  RoughCalcType rough_type_sea{RoughCalcType::CHARNOCK};
  PBLHeightCalcType pblh_type{PBLHeightCalcType::None};
 
private:
  // Set in constructor
  amrex::Vector<amrex::Geometry> m_geom;
  bool m_rotate = false;
  double m_start_low_time;
  double m_final_low_time;
  double m_low_time_interval;
 
  bool m_include_wstar = false;
  amrex::Real z0_const{amrex::Real(0.1)};
  amrex::Real default_land_surf_temp{amrex::Real(300.)};
  amrex::Real surf_temp;
  amrex::Real surf_heating_rate{0};
  amrex::Real surf_temp_flux{0};
  amrex::Real default_land_surf_moist{zero};
  amrex::Real surf_moist;
  amrex::Real surf_moist_flux{0};
  amrex::Real custom_ustar{0};
  amrex::Real custom_tstar{0};
  amrex::Real custom_qstar{0};
  amrex::Real custom_rhosurf{0}; // use specified value instead of rho from first cell
  bool specified_rho_surf{false};
  amrex::Real cnk_a{amrex::Real(0.0185)};
  bool cnk_visc{false};
  amrex::Real depth{amrex::Real(30.0)};
  amrex::Vector<amrex::MultiFab> z_0;
  bool m_var_z0{false};
 
  amrex::Real rico_theta_z0{amrex::Real(298.0)};
  amrex::Real rico_qsat_z0{amrex::Real(0.001)};
 
  bool use_moisture;
  bool m_has_lsm_fluxes = false;
  bool m_has_lsm_tsurf  = false;
  bool m_has_ocean_lsm_tsurf = false;
  int  m_lsm_tsurf_indx = -1;
 
  amrex::Real m_Cd = zero;
  amrex::Real m_Ch = zero;
  amrex::Real m_Cq = zero;
 
  bool m_ignore_sst = false;
 
  amrex::Vector<const eb_*> m_eb_vec;
  TerrainType m_terrain_type;
  MOSTAverage m_ma;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> u_star;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> w_star;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> t_star;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> q_star;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> olen;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> pblh;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> t_surf;
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> q_surf;
  // Diagnostic-only provenance mask. This records the cell-centered source
  // path used by the SurfaceLayer scalar diagnostic path. It must not feed
  // back into flux calculations, boundary conditions, or model state.
  amrex::Vector<std::unique_ptr<amrex::MultiFab>> surface_diagnostic_source;
 
  amrex::Vector<amrex::Vector<amrex::MultiFab*>>  m_sst_lev;
  amrex::Vector<amrex::Vector<amrex::MultiFab*>>  m_tsk_lev;
  amrex::Vector<amrex::Vector<amrex::iMultiFab*>> m_lmask_lev;
  amrex::Vector<amrex::Vector<amrex::MultiFab*>>  m_lsm_data_lev;
  amrex::Vector<amrex::Vector<amrex::MultiFab*>>  m_lsm_flux_lev;
  amrex::Vector<std::string> m_lsm_data_name;
  amrex::Vector<std::string> m_lsm_flux_name;
  amrex::Vector<amrex::MultiFab*> m_Hwave_lev;
  amrex::Vector<amrex::MultiFab*> m_Lwave_lev;
  amrex::Vector<amrex::MultiFab*> m_eddyDiffs_lev;
 
  bool m_update_k_rans = false;
  amrex::Real inv_Cmu2 = zero;
  amrex::Real theta_ref = zero;
};
 
#endif /* SURFACELAYER_H */