ERF_InputSoundingData.H

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#ifndef ERF_INPUT_SOUNDING_DATA_H_
#define ERF_INPUT_SOUNDING_DATA_H_
 
#include <string>
#include <iostream>
 
#include <AMReX_ParmParse.H>
#include <AMReX_Print.H>
#include <AMReX_Gpu.H>
#include <AMReX_Geometry.H>
 
#include <ERF_EOS.H>
#include <ERF_Constants.H>
#include <ERF_Interpolation_1D.H>
#include <ERF_HSEUtils.H>
 
/**
 * Data structure storing input sounding data. Also
 * handles reading the input file for sounding data and
 * hydrostatic column integration.
 */
struct InputSoundingData {
public:
    /**
     * @brief Construct input sounding metadata from the ERF input namespace.
     */
    InputSoundingData ()
    {
        amrex::ParmParse pp("erf");
        pp.query("tau_nudging", tau_nudging);
 
        // Read in input_sounding filename
        n_sounding_files = pp.countval("input_sounding_file");
        if (n_sounding_files > 0) {
            input_sounding_file.resize(n_sounding_files);
            pp.queryarr("input_sounding_file", input_sounding_file, 0, n_sounding_files);
        } else {
            n_sounding_files = 1;
            input_sounding_file.resize(n_sounding_files);
            input_sounding_file[0] = "input_sounding";
        }
 
        // Read in input_sounding times
        n_sounding_times = pp.countval("input_sounding_time");
 
        if (n_sounding_times > 0) {
            input_sounding_time.resize(n_sounding_times);
            pp.queryarr("input_sounding_time", input_sounding_time, 0, n_sounding_times);
        } else {
            n_sounding_times = 1;
            input_sounding_time.resize(n_sounding_times);
            input_sounding_time[0] = zero;
        }
 
        // If we have more files than times or times than files we just use the minimum
        int n = std::min(n_sounding_times, n_sounding_files);
        n_sounding_files = n;
        n_sounding_times = n;
        input_sounding_file.resize(n);
        input_sounding_time.resize(n);
    }
 
    /**
     * @brief Resize host and device sounding arrays for the configured sounding times.
     */
    void resize_arrays ()
    {
        ntimes = n_sounding_files;
 
        z_inp_sound.resize(ntimes);
        theta_inp_sound.resize(ntimes);
        qv_inp_sound.resize(ntimes);
        U_inp_sound.resize(ntimes);
        V_inp_sound.resize(ntimes);
 
        z_inp_sound_d.resize(ntimes);
        theta_inp_sound_d.resize(ntimes);
        qv_inp_sound_d.resize(ntimes);
        U_inp_sound_d.resize(ntimes);
        V_inp_sound_d.resize(ntimes);
    }
 
    /**
     * @brief Read and interpolate one input sounding profile onto level-0 heights.
     * @param geom Geometry defining the level-0 vertical domain.
     * @param zlevels_stag Staggered vertical coordinates used for interpolation.
     * @param itime Sounding time/file index to read.
     * @param is_moist Whether the selected physics permits nonzero water vapor.
     */
    void read_from_file (const amrex::Geometry &geom,
                         const amrex::Vector<amrex::Real>& zlevels_stag,
                         int itime, bool is_moist)
    {
        const int klo = 0;
        const int khi = geom.Domain().bigEnd()[AMREX_SPACEDIM-1];
        const int Nz = geom.Domain().size()[AMREX_SPACEDIM-1];
 
        const amrex::Real zbot = zlevels_stag[klo];
        const amrex::Real ztop = zlevels_stag[khi+1];
 
        z_inp_sound[itime].resize(Nz+2);
        theta_inp_sound[itime].resize(Nz+2);
        qv_inp_sound[itime].resize(Nz+2);
        U_inp_sound[itime].resize(Nz+2);
        V_inp_sound[itime].resize(Nz+2);
 
        // Read the input_sounding file
        amrex::Print() << "input_sounding file location : " << input_sounding_file[itime] << std::endl;
        std::ifstream input_sounding_reader(input_sounding_file[itime]);
        if(!input_sounding_reader.is_open()) {
            amrex::Error("Error opening the input_sounding file\n");
        }
        else {
            // Read the contents of the input_sounding file
            amrex::Print() << "Successfully opened the input_sounding file. Now reading... " << std::endl;
            std::string line;
 
            // First, read the input data into temp vectors; then, interpolate vectors to the
            // domain lo/hi and cell centers (from level 0)
            amrex::Vector<amrex::Real> z_inp_sound_tmp, theta_inp_sound_tmp, qv_inp_sound_tmp,
                                       U_inp_sound_tmp, V_inp_sound_tmp;
 
            // Read surface quantities from the first line
            std::getline(input_sounding_reader, line);
            std::istringstream iss(line);
            iss >> press_ref_inp_sound >> theta_ref_inp_sound >> qv_ref_inp_sound;
            press_ref_inp_sound *= 100; // convert from hPa to Pa
            qv_ref_inp_sound *= amrex::Real(0.001); // convert from g/kg to kg/kg
 
            // Add surface
            z_inp_sound_tmp.push_back(zbot); // height above sea level [m]
            theta_inp_sound_tmp.push_back(theta_ref_inp_sound);
            qv_inp_sound_tmp.push_back(qv_ref_inp_sound);
            U_inp_sound_tmp.push_back(0);
            V_inp_sound_tmp.push_back(0);
 
            // *************************************************************************************************
            // Make sure that if we specify surface values for temp in the inputs file and in the input sounding file,
            //      those values must match
            // *************************************************************************************************
            amrex::ParmParse pp_erf("erf");
 
            amrex::Real surf_temp;
            bool surf_temp_specified = pp_erf.query("most.surf_temp", surf_temp);
            if ( surf_temp_specified && (surf_temp != theta_inp_sound_tmp[0]) ) {
                amrex::Print() << "Input sounding temp does not match most.surf_temp" << std::endl;
                amrex::Print() << "Modify one or both to match." << std::endl;
                amrex::Abort();
            }
 
            // *************************************************************************************************
            // Make sure that if we specify surface values for qv in the inputs file and in the input sounding file,
            //      those values must match
            // *************************************************************************************************
            amrex::Real surf_moist;
            bool surf_moist_specified = pp_erf.query("most.surf_moist", surf_moist);
            if ( surf_moist_specified && (surf_moist != qv_inp_sound_tmp[0]) ) {
                amrex::Print() << "Input sounding qv does not match most.surf_moist" << std::endl;
                amrex::Print() << "Modify one or both to match." << std::endl;
                amrex::Abort();
            }
 
            // Read the vertical profile at each given height
            amrex::Real z, theta, qv, U, V;
 
            while(std::getline(input_sounding_reader, line)) {
                std::istringstream iss_z(line);
                iss_z >> z >> theta >> qv >> U >> V;
 
                // Dont read in non-zero qv if not using a moisture model
                AMREX_ALWAYS_ASSERT(qv == zero || is_moist);
 
                if (z == zbot) {
                    AMREX_ALWAYS_ASSERT(theta == theta_inp_sound_tmp[0]);
                    AMREX_ALWAYS_ASSERT(qv*amrex::Real(0.001) == qv_inp_sound_tmp[0]); // convert from g/kg to kg/kg
                    U_inp_sound_tmp[0] = U;
                    V_inp_sound_tmp[0] = V;
                } else {
                    AMREX_ALWAYS_ASSERT(z > z_inp_sound_tmp[z_inp_sound_tmp.size()-1]); // sounding is increasing in height
                    z_inp_sound_tmp.push_back(z);
 
                    theta_inp_sound_tmp.push_back(theta);
                    qv_inp_sound_tmp.push_back(qv*amrex::Real(0.001)); // convert from g/kg to kg/kg
                    U_inp_sound_tmp.push_back(U);
                    V_inp_sound_tmp.push_back(V);
                    if (z >= ztop) break;
                }
            }
 
            // At this point, we have an input_sounding from zbot up to
            // z_inp_sound_tmp[N-1] >= ztop. Now, interpolate to grid level 0 heights
            const int Ninp = z_inp_sound_tmp.size();
            z_inp_sound[itime][0]     = zbot;
            theta_inp_sound[itime][0] = theta_inp_sound_tmp[0];
            qv_inp_sound[itime][0]    = qv_inp_sound_tmp[0];
            U_inp_sound[itime][0]     = U_inp_sound_tmp[0];
            V_inp_sound[itime][0]     = V_inp_sound_tmp[0];
            for (int k=0; k < Nz; ++k) {
                z_inp_sound[itime][k+1] = myhalf * (zlevels_stag[k] + zlevels_stag[k+1]);
                theta_inp_sound[itime][k+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(), theta_inp_sound_tmp.dataPtr(), z_inp_sound[itime][k+1], Ninp);
                   qv_inp_sound[itime][k+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(),    qv_inp_sound_tmp.dataPtr(), z_inp_sound[itime][k+1], Ninp);
                    U_inp_sound[itime][k+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(),     U_inp_sound_tmp.dataPtr(), z_inp_sound[itime][k+1], Ninp);
                    V_inp_sound[itime][k+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(),     V_inp_sound_tmp.dataPtr(), z_inp_sound[itime][k+1], Ninp);
            }
            z_inp_sound[itime][Nz+1]     = ztop;
            theta_inp_sound[itime][Nz+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(), theta_inp_sound_tmp.dataPtr(), ztop, Ninp);
               qv_inp_sound[itime][Nz+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(),    qv_inp_sound_tmp.dataPtr(), ztop, Ninp);
                U_inp_sound[itime][Nz+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(),     U_inp_sound_tmp.dataPtr(), ztop, Ninp);
                V_inp_sound[itime][Nz+1] = interpolate_1d(z_inp_sound_tmp.dataPtr(),     V_inp_sound_tmp.dataPtr(), ztop, Ninp);
        }
 
        amrex::Print() << "Successfully read the " << itime << "th input_sounding file..." << std::endl;
        input_sounding_reader.close();
 
        host_to_device(itime);
    }
 
    /**
     * @brief Hydrostatically integrate density and pressure for one sounding.
     * @param itime Sounding time/file index to integrate.
     */
    void calc_rho_p (int itime)
    {
        /* Calculate density and pressure, roughly following the procedure in
         * WRF dyn_em/module_initialize_ideal.F. We integrate hydrostatically
         * from the surface up through the air column to get the dry density
         * and moist pressure.
         */
        const amrex::Real tol = amrex::Real(1.0e-12);
        const int Ninp = size(itime);
        pm_integ.resize(Ninp);
        rhod_integ.resize(Ninp);
 
        // evaluate surface quantities (k=0): total pressure and dry air
          pm_integ[0] = press_ref_inp_sound;
        rhod_integ[0] = getRhogivenThetaPress(theta_ref_inp_sound,
                                              press_ref_inp_sound,
                                              RdoCp,
                                              qv_ref_inp_sound);
 
        amrex::Print() << "ideal sounding init: surface dry air density = "
                       << std::setprecision(15)
                       << rhod_integ[0] << " kg/m^3" << std::endl;
 
        // Note:
        //   p_dry = rho_d R_d T
        //   p_tot = rho_m R_d T_v
        //         = rho_d(1 + q_v) R_d T_v
 
#if 0   // Printing
        // In this absence of moisture, this moist profile will match the
        // following dry profile
        amrex::Print() << "z  p_m  rho_d  theta  qv  U  V" << std::endl;
        amrex::Print() << z_inp_sound[itime][0]
                       << " " << pm_integ[0]
                       << " " << rhod_integ[0]
                       << " " << theta_inp_sound[itime][0]
                       << " " << qv_inp_sound[itime][0]
                       << " " << U_inp_sound[itime][0]
                       << " " << V_inp_sound[itime][0]
                       << std::endl;
#endif
 
         // integrate from surface to domain top
        amrex::Real dz, F, C;
        amrex::Real T_hi;
        amrex::Real rho_tot_hi, rho_tot_lo;
        for (int k=1; k < size(itime); ++k)
        {
            // Vertical grid spacing
            dz = z_inp_sound[itime][k] - z_inp_sound[itime][k-1];
 
            // Establish known constant
            rho_tot_lo = rhod_integ[k-1] * (one + qv_inp_sound[itime][k-1]);
            C  = -pm_integ[k-1] + myhalf*rho_tot_lo*CONST_GRAV*dz;
 
            // Initial guess and residual
            pm_integ[k]   = pm_integ[k-1];
            T_hi          = getTgivenPandTh(pm_integ[k], theta_inp_sound[itime][k], RdoCp);
            rhod_integ[k] = getRhogivenThetaPress(theta_inp_sound[itime][k],
                                                  pm_integ[k],
                                                  RdoCp,
                                                  qv_inp_sound[itime][k]);
            rho_tot_hi = rhod_integ[k] * (one + qv_inp_sound[itime][k]);
            F = pm_integ[k] + myhalf*rho_tot_hi*CONST_GRAV*dz + C;
 
            // Do iterations
            if (std::abs(F)>tol) {
                bool maintain_Th = true;
                HSEutils::Newton_Raphson_hse(tol, RdoCp, dz,
                                             CONST_GRAV, C, theta_inp_sound[itime][k], T_hi,
                                             qv_inp_sound[itime][k], qv_inp_sound[itime][k],
                                             pm_integ[k], rhod_integ[k], F, maintain_Th);
            }
 
#if 0       // Printing
            amrex::Print() << z_inp_sound[itime][k]
                           << " " << pm_integ[k]
                           << " " << rhod_integ[k]
                           << " " << theta_inp_sound[itime][k]
                           << " " << qv_inp_sound[itime][k]
                           << " " << U_inp_sound[itime][k]
                           << " " << V_inp_sound[itime][k]
                           << std::endl;
#endif
        }
        // Note: at this point, the surface pressure, density of the dry air
        // column is stored in pm_integ[0], rhod_integ[0]
 
        // update
        host_to_device(itime);
    }
 
    /**
     * @brief Compute density and pressure for an isentropic sounding profile.
     * @param itime Sounding time/file index to integrate.
     */
    void calc_rho_p_isentropic (int itime)
    {
        /* Calculate density and pressure assuming isentropic (constant theta)
           background conditions. This does not use Newton-Raphson iterations
           to calculate rho and p.
         */
        const int Ninp = size(itime);
        pm_integ.resize(Ninp);
        rhod_integ.resize(Ninp);
 
        // evaluate surface quantities (k=0): total pressure and dry air
        pm_integ[0]   = press_ref_inp_sound;
        rhod_integ[0] = getRhogivenThetaPress(theta_ref_inp_sound,
                                              press_ref_inp_sound,
                                              RdoCp,
                                              qv_ref_inp_sound);
 
        const amrex::Real th0 = theta_ref_inp_sound;
        const amrex::Real p0_pow = std::pow(p_0, (Gamma-1)/Gamma);
 
        amrex::Print() << "isentropic sounding init: surface dry air density = "
                       << std::setprecision(15)
                       << rhod_integ[0] << " kg/m^3" << std::endl;
 
#if 0   // Printing
        // In this absence of moisture, this moist profile will match the
        // following dry profile
        amrex::Print() << "z  p_m  rho_d  theta  qv  U  V" << std::endl;
        amrex::Print() << z_inp_sound[itime][0]
                       << " " << pm_integ[0]
                       << " " << rhod_integ[0]
                       << " " << theta_inp_sound[itime][0]
                       << " " << qv_inp_sound[itime][0]
                       << " " << U_inp_sound[itime][0]
                       << " " << V_inp_sound[itime][0]
                       << std::endl;
#endif
 
         // integrate from surface to domain top
        amrex::Real dz;
        for (int k=1; k < size(itime); ++k)
        {
            // Vertical grid spacing
            dz = z_inp_sound[itime][k] - z_inp_sound[itime][k-1];
 
            // Isentropic pressure at next level
            amrex::Real qvmean = (assume_dry) ? zero : myhalf*(qv_inp_sound[itime][k-1] + qv_inp_sound[itime][k]);
            amrex::Real thm0 = th0 * (one + RvoRd * qvmean);
            amrex::Real plo_pow = std::pow(pm_integ[k-1], (Gamma-1)/Gamma);
            pm_integ[k] = (Gamma-1)/Gamma *
                (-CONST_GRAV * p0_pow / (R_d * thm0) * (1 + qvmean) * dz
                 + Gamma/(Gamma-1) * plo_pow);
            pm_integ[k] = std::pow(pm_integ[k], Gamma / (Gamma-1));
 
            // Note: The pressure calculated here is copied to `p_inp_sound_d`
            // and currently not used.
 
            // Get corresponding dry air density
            rhod_integ[k] = getRhogivenThetaPress(theta_inp_sound[itime][k],
                                                  pm_integ[k],
                                                  RdoCp,
                                                  qv_inp_sound[itime][k]);
 
#if 0       // Printing
            amrex::Print() << z_inp_sound[itime][k]
                           << " " << pm_integ[k]
                           << " " << rhod_integ[k]
                           << " " << theta_inp_sound[itime][k]
                           << " " << qv_inp_sound[itime][k]
                           << " " << U_inp_sound[itime][k]
                           << " " << V_inp_sound[itime][k]
                           << std::endl;
#endif
        }
        // Note: at this point, the surface pressure, density of the dry air
        // column is stored in pm_integ[0], rhod_integ[0]
 
        // update
        host_to_device(itime);
    }
 
    /**
     * @brief Copy host sounding arrays for one time index to device storage.
     * @param itime Sounding time/file index to copy.
     */
    void host_to_device (int itime)
    {
        const int Ninp = size(itime);
        z_inp_sound_d[itime].resize(Ninp);
        theta_inp_sound_d[itime].resize(Ninp);
        qv_inp_sound_d[itime].resize(Ninp);
        U_inp_sound_d[itime].resize(Ninp);
        V_inp_sound_d[itime].resize(Ninp);
 
        amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                         z_inp_sound[itime].begin(), z_inp_sound[itime].end(),
                         z_inp_sound_d[itime].begin());
        amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                         theta_inp_sound[itime].begin(), theta_inp_sound[itime].end(),
                         theta_inp_sound_d[itime].begin());
        amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                         qv_inp_sound[itime].begin(), qv_inp_sound[itime].end(),
                         qv_inp_sound_d[itime].begin());
        amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                         U_inp_sound[itime].begin(), U_inp_sound[itime].end(),
                         U_inp_sound_d[itime].begin());
        amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                         V_inp_sound[itime].begin(), V_inp_sound[itime].end(),
                         V_inp_sound_d[itime].begin());
 
        if (rhod_integ.size() > 0)
        {
            //amrex::Print() << "Copying rho_d, p_d to device" << std::endl;
            rho_inp_sound_d.resize(size(itime)+2);
            p_inp_sound_d.resize(size(itime)+2);
            amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                             rhod_integ.begin(), rhod_integ.end(),
                             rho_inp_sound_d.begin());
            amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                             pm_integ.begin(), pm_integ.end(),
                             p_inp_sound_d.begin());
        }
    }
 
    /**
     * @brief Return the number of interpolated samples for one sounding time.
     * @param itime Sounding time/file index to query.
     * @return Number of stored sounding profile levels.
     */
    int size (int itime) const
    {
        AMREX_ALWAYS_ASSERT(z_inp_sound[itime].size() == theta_inp_sound[itime].size());
        AMREX_ALWAYS_ASSERT(z_inp_sound[itime].size() == qv_inp_sound[itime].size());
        AMREX_ALWAYS_ASSERT(z_inp_sound[itime].size() == U_inp_sound[itime].size());
        AMREX_ALWAYS_ASSERT(z_inp_sound[itime].size() == V_inp_sound[itime].size());
        return z_inp_sound[itime].size();
    }
 
    // Members
    int ntimes;
 
    amrex::Real tau_nudging = amrex::Real(5.0); // time scale used for nudging
 
    amrex::Vector<std::string> input_sounding_file = {};
    amrex::Vector<amrex::Real> input_sounding_time = {};
    int n_sounding_files = 0;
    int n_sounding_times = 0;
 
    bool assume_dry{false};
 
    // - read from file
    amrex::Real press_ref_inp_sound, theta_ref_inp_sound, qv_ref_inp_sound; // input
 
    // This is a vector (over time) of Vectors
    amrex::Vector<amrex::Vector<amrex::Real>> z_inp_sound, theta_inp_sound, qv_inp_sound, U_inp_sound, V_inp_sound;
 
    // This is a vector (over time) of DeviceVectors
    amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> z_inp_sound_d, theta_inp_sound_d, qv_inp_sound_d, U_inp_sound_d, V_inp_sound_d;
 
    // - moist profiles
    amrex::Vector<amrex::Real> pm_integ; // from integrating up air column
    // - dry profiles
    amrex::Vector<amrex::Real> rhod_integ; // from integrating down air column
    // - to set solution fields
    amrex::Gpu::DeviceVector<amrex::Real> p_inp_sound_d, rho_inp_sound_d;
};
 
/**
 * @var InputSoundingData::ntimes
 * @brief Number of sounding times represented in the arrays.
 * @var InputSoundingData::tau_nudging
 * @brief Nudging time scale for relaxing toward input sounding data.
 * @var InputSoundingData::input_sounding_file
 * @brief Sounding file path for each configured sounding time.
 * @var InputSoundingData::input_sounding_time
 * @brief Physical time associated with each input sounding file.
 * @var InputSoundingData::n_sounding_files
 * @brief Number of input sounding files.
 * @var InputSoundingData::n_sounding_times
 * @brief Number of input sounding times.
 * @var InputSoundingData::assume_dry
 * @brief Whether to ignore moisture in isentropic pressure integration.
 * @var InputSoundingData::press_ref_inp_sound
 * @brief Surface reference pressure read from the input sounding [Pa].
 * @var InputSoundingData::theta_ref_inp_sound
 * @brief Surface reference potential temperature read from the input sounding [K].
 * @var InputSoundingData::qv_ref_inp_sound
 * @brief Surface reference water vapor mixing ratio read from the input sounding [kg/kg].
 * @var InputSoundingData::z_inp_sound
 * @brief Interpolated host sounding heights for each sounding time [m].
 * @var InputSoundingData::theta_inp_sound
 * @brief Interpolated host potential temperature profiles [K].
 * @var InputSoundingData::qv_inp_sound
 * @brief Interpolated host water vapor mixing ratio profiles [kg/kg].
 * @var InputSoundingData::U_inp_sound
 * @brief Interpolated host x velocity profiles.
 * @var InputSoundingData::V_inp_sound
 * @brief Interpolated host y velocity profiles.
 * @var InputSoundingData::z_inp_sound_d
 * @brief Device sounding heights for each sounding time [m].
 * @var InputSoundingData::theta_inp_sound_d
 * @brief Device potential temperature profiles [K].
 * @var InputSoundingData::qv_inp_sound_d
 * @brief Device water vapor mixing ratio profiles [kg/kg].
 * @var InputSoundingData::U_inp_sound_d
 * @brief Device x velocity profiles.
 * @var InputSoundingData::V_inp_sound_d
 * @brief Device y velocity profiles.
 * @var InputSoundingData::pm_integ
 * @brief Hydrostatically integrated moist pressure profile.
 * @var InputSoundingData::rhod_integ
 * @brief Hydrostatically integrated dry density profile.
 * @var InputSoundingData::p_inp_sound_d
 * @brief Device pressure profile used to initialize solution fields.
 * @var InputSoundingData::rho_inp_sound_d
 * @brief Device density profile used to initialize solution fields.
 */
#endif