ERF_NCWpsFile.H

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/**
 * \file ERF_NCWpsFile.H
 */
#ifndef ERF_NCWPSFILE_H_
#define ERF_NCWPSFILE_H_
 
#include <sstream>
#include <string>
#include <atomic>
 
#include "AMReX_FArrayBox.H"
#include "AMReX_IArrayBox.H"
#include "ERF_EpochTime.H"
#include "ERF_NCInterface.H"
 
using PlaneVector = amrex::Vector<amrex::FArrayBox>;
 
/*
 // Read from metgrid
 NetCDF variables of dimensions Time_BT_SN_WE: "UU", "VV", "TT", "RH", "PRES", "GHT"
 NetCDF variables of dimensions Time_SN_WE   : "HGT", "MAPFAC_U",  "MAPFAC_V",  "MAPFAC_M", "PSFC"
 NetCDF global attributes of type int        : "WEST-EAST_GRID_DIMENSION", "SOUTH-NORTH_GRID_DIMENSION"
 NetCDF global attributes of type string     : "SIMULATION_START_DATE"
 NetCDF global attributes of type real       : "DX", "DY"
 
 // Read from wrfbdy
 NetCDF variables of dimensions Time_BdyWidth_BT_SN         : "U_BXS", "U_BXE", "V_BXS", "V_BXE" etc.
 NetCDF variables of dimensions Time_BdyWidth_BT_WE         : "U_BYS", "U_BYE", "V_BYS", "V_BYE" etc.
 NetCDF variables of dimensions Time_BdyWidth_SN            : "MU_BXS", "MU_BXE", "PC_BXS", "PC_BXE", etc.
 NetCDF variables of dimensions Time_BdyWidth_WE            : "MU_BYS", "MU_BYE", "PC_BYS", "PC_BYE", etc.
*/
enum class NC_Data_Dims_Type {
    Time_SL_SN_WE,       // Time, Soil Layers, South-North, West-East
    Time_BT_SN_WE,
    Time_SN_WE,
    Time_BT,
    Time_SL,             // Time, Soil layers
    Time,
    Time_BdyWidth_BT_SN,
    Time_BdyWidth_BT_WE,
    Time_BdyWidth_SN,
    Time_BdyWidth_WE
};
 
//
// NDArray is the datatype designed to hold any data, including scalars, multidimensional
// arrays, that read from the NetCDF file.
//
// The data read from NetCDF file are stored in a continuous memory, and the data layout is described
// by using a vector (shape). AMReX Box can be constructed using the data shape information, and MultiFab
// data array can be setup using the data that stored in the NDArray.
//
template <typename DataType>
struct NDArray
{
   using DType = typename std::remove_const<DataType>::type;
 
   // constructor
   explicit NDArray (const std::string vname, const std::vector<size_t>& vshape)
                    : name{vname}, shape{vshape},
                      data{std::shared_ptr<DType[]>(new DType[this->ndim()],
                                                   std::default_delete<DType[]>())} {}
 
   // default constructor
   NDArray () : name{"null"}, data{nullptr} {}
 
   // get the data pointer
   decltype(auto) get_data () {
     return data.get();
   }
 
   // get the variable name
   std::string get_vname () {
     return name;
   }
 
   // get the variable data shape
   std::vector<size_t> get_vshape () {
     return shape;
   }
 
   // return the total number of data
   size_t ndim () {
     size_t num = 1;
     int isize = static_cast<int>(shape.size());
     for (auto i=0; i<isize; ++i) num *= shape[i];
     return num;
   }
 
   // set the data shape information
   void set_vshape (std::vector<size_t> vshape) {
     shape = vshape;
    }
 
 private:
   std::string name;
   std::vector<size_t> shape;
   std::shared_ptr<DType[]> data;
};
 
int BuildFABsFromWRFBdyFile (const std::string &fname,
                             amrex::Vector<amrex::Vector<amrex::FArrayBox>>& bdy_data_xlo,
                             amrex::Vector<amrex::Vector<amrex::FArrayBox>>& bdy_data_xhi,
                             amrex::Vector<amrex::Vector<amrex::FArrayBox>>& bdy_data_ylo,
                             amrex::Vector<amrex::Vector<amrex::FArrayBox>>& bdy_data_yhi);
 
template<typename DType>
void ReadTimeSliceFromNetCDFFile (const std::string& fname,
                                  const int tidx,
                                  amrex::Vector<std::string> names,
                                  amrex::Vector<NDArray<DType> >& arrays,
                                  amrex::Vector<int>& success)
{
    amrex::Print() << "Reading time slice " << tidx << " from " << fname << std::endl;
    AMREX_ASSERT(arrays.size() == names.size());
 
    if (amrex::ParallelDescriptor::IOProcessor())
    {
        auto ncf = ncutils::NCFile::open(fname, NC_CLOBBER | NC_NETCDF4);
 
        int ntimes = ncf.dim("Time").len();
        AMREX_ALWAYS_ASSERT((tidx >= 0) && (tidx < ntimes));
 
        for (auto n=0; n<arrays.size(); ++n)
        {
            std::string vname_to_write = names[n];
            std::string vname_to_read  = names[n];
            if (vname_to_read.substr(0,2) == "R_") {
                vname_to_read  = names[n+4]; // This allows us to read "T" instead -- we will over-write this later
            }
 
            success[n] = ncf.has_var(vname_to_read);
 
            if (success[n] == 1)
            {
                std::vector<std::string> dimnames = ncf.var(vname_to_read).dimnames();
                AMREX_ALWAYS_ASSERT(dimnames[0] == "Time");
 
                std::vector<size_t> count = ncf.var(vname_to_read).shape();
                std::vector<size_t> start(count.size(), 0);
                start[0] = tidx;
                count[0] = 1;
 
                arrays[n] = NDArray<DType>(vname_to_read, count);
                DType* dataPtr = arrays[n].get_data();
 
                ncf.var(vname_to_read).get(dataPtr, start, count);
            } // has_var
        }
        ncf.close();
    }
}
 
template<typename DType>
void ReadNetCDFFile (const std::string& fname, amrex::Vector<std::string> names,
                     amrex::Vector<NDArray<DType> >& arrays, amrex::Vector<int>& success)
{
    AMREX_ASSERT(arrays.size() == names.size());
 
    if (amrex::ParallelDescriptor::IOProcessor())
    {
        auto ncf = ncutils::NCFile::open(fname, NC_CLOBBER | NC_NETCDF4);
 
        /*
        // get the dimension information
        int Time               = static_cast<int>(ncf.dim("Time").len());
        int DateStrLen         = static_cast<int>(ncf.dim("DateStrLen").len());
        int west_east          = static_cast<int>(ncf.dim("west_east").len());
        int south_north        = static_cast<int>(ncf.dim("south_north").len());
        int bottom_top         = static_cast<int>(ncf.dim("bottom_top").len());
        int bottom_top_stag    = static_cast<int>(ncf.dim("bottom_top_stag").len());
        int west_east_stag     = static_cast<int>(ncf.dim("west_east_stag").len());
        int south_north_stag   = static_cast<int>(ncf.dim("south_north_stag").len());
        int bdy_width          = static_cast<int>(ncf.dim("bdy_width").len());
        */
 
        // amrex::Print() << "Reading the dimensions from the netcdf file " << "\n";
 
        for (auto n=0; n<arrays.size(); ++n)
        {
            std::string vname_to_write = names[n];
            std::string vname_to_read  = names[n];
 
            if (vname_to_read.substr(0,2) == "R_") {
                vname_to_read  = names[n+4]; // This allows us to read "T" instead -- we will over-write this later
            }
 
            success[n] = ncf.has_var(vname_to_read);
            if (success[n] == 0) {
                amrex::Print() << " Skipping " << vname_to_read << std::endl;
            } else {
                amrex::Print() << " Reading  " << vname_to_read << std::endl;
            }
 
            if (success[n] == 1) {
 
                std::vector<std::string> dimnames = ncf.var(vname_to_read).dimnames();
                AMREX_ALWAYS_ASSERT(dimnames[0] == "Time" || dimnames[0] == "time");
 
                std::vector<size_t> shape = ncf.var(vname_to_read).shape();
                arrays[n]                 = NDArray<DType>(vname_to_read,shape);
                DType* dataPtr            = arrays[n].get_data();
 
                std::vector<size_t> start(shape.size(), 0);
 
#if 0
                auto numPts               = arrays[n].ndim();
                amrex::Print() << "NetCDF Variable name = " << vname_to_read << std::endl;
                amrex::Print() << "numPts read from NetCDF file/var = " << numPts << std::endl;
                amrex::Print() << "Dims in var = " << ncf.var(vname_to_read).ndim() << std::endl;
                amrex::Print()  << "Dim names = (";
                for (auto &dim:dimnames)
                    amrex::Print() << dim << ", " ;
                amrex::Print()  << ")" << std::endl;
                amrex::Print()  << "Dims of the variable = (";
                for (auto &dim:shape)
                    amrex::Print() << dim << ", " ;
                amrex::Print()  << ")" << std::endl;
#endif
 
                ncf.var(vname_to_read).get(dataPtr, start, shape);
 
            } // has_var
        }
        ncf.close();
    }
}
 
/**
 * Helper function for reading data from NetCDF file into a
 * provided FAB.
 *
 * @param iv Index for which variable we are going to fill
 * @param domain Box specifying the horizontal and vertical extent to read
 * @param nc_arrays Arrays of data from NetCDF file
 * @param var_name Variable name
 * @param NC_dim_type Dimension type for the variable as stored in the NetCDF file
 * @param temp FAB where we store the variable data from the NetCDF Arrays
 */
template<class FAB,typename DType>
void
fill_fab_from_arrays (int iv,
                      const amrex::Box& domain,
                      amrex::Vector<NDArray<float>>& nc_arrays,
                      const std::string& var_name,
                      NC_Data_Dims_Type& NC_dim_type,
                      FAB& temp)
{
    int ns1, ns2, ns3; // bottom_top, south_north, west_east (these can be staggered or unstaggered)
    if (NC_dim_type == NC_Data_Dims_Type::Time_BT) {
        ns1 = nc_arrays[iv].get_vshape()[1];
        ns2 = 1;
        ns3 = 1;
        // amrex::Print() << "TYPE BT " << ns1 << std::endl;
    } else if (NC_dim_type == NC_Data_Dims_Type::Time_SN_WE) {
        ns1 = 1;
        ns2 = nc_arrays[iv].get_vshape()[1];
        ns3 = nc_arrays[iv].get_vshape()[2];
        // amrex::Print() << "TYPE SN WE " << ns2 << " " << ns3 << std::endl;
    } else if (NC_dim_type == NC_Data_Dims_Type::Time_BT_SN_WE) {
        ns1 = nc_arrays[iv].get_vshape()[1];
        ns2 = nc_arrays[iv].get_vshape()[2];
        ns3 = nc_arrays[iv].get_vshape()[3];
        // amrex::Print() << "TYPE BT SN WE " << ns1 << " " << ns2 << " " << ns3 << std::endl;
    } else if (NC_dim_type == NC_Data_Dims_Type::Time_SL_SN_WE) {
        ns1 = nc_arrays[iv].get_vshape()[1];
        ns2 = nc_arrays[iv].get_vshape()[2];
        ns3 = nc_arrays[iv].get_vshape()[3];
        // amrex::Print() << "TYPE SL SN WE " << ns1 << " " << ns2 << " " << ns3 << std::endl;
    } else if (NC_dim_type == NC_Data_Dims_Type::Time_SL) {
        ns1 = nc_arrays[iv].get_vshape()[1];
        ns2 = 1;
        ns3 = 1;
        // amrex::Print() << "TYPE SL " << ns1 << std::endl;
    }
    else {
        amrex::Abort("Dont know this NC_Data_Dims_Type");
    }
 
    // allow fewer z levels to be read in
    // - ns1 may be the bottom_top or bottom_top_stag dim
    // - domain.bigEnd(2) is the input number of cells in z
    // - khi may be nz==bottom_top, nz < bottom_top, or 0 for 2D fields
    int khi = std::min(domain.bigEnd(2), ns1-1);
 
    // TODO:  The box will only start at (0,0,0) at level 0 -- we need to generalize this
    amrex::Box in_box(amrex::IntVect(0,0,0), amrex::IntVect(ns3-1,ns2-1,ns1-1)); // ns1 may or may not be staggered
    amrex::Box my_box(amrex::IntVect(0,0,0), amrex::IntVect(ns3-1,ns2-1,khi));
 
    if (var_name == "PH" || var_name == "PHB") {
        my_box.setType(amrex::IndexType(amrex::IntVect(0,0,1)));
        my_box.setBig(2, khi+1);
    }
    else if (var_name == "U" || var_name == "UU" || var_name == "MAPFAC_U") {
        my_box.setType(amrex::IndexType(amrex::IntVect(1,0,0)));
    }
    else if (var_name == "V" || var_name == "VV" || var_name == "MAPFAC_V") {
        my_box.setType(amrex::IndexType(amrex::IntVect(0,1,0)));
    }
    else if (var_name == "W" || var_name == "WW") {
        my_box.setType(amrex::IndexType(amrex::IntVect(0,0,1)));
        my_box.setBig(2, khi+1);
    }
    else if (var_name == "TSLB" || var_name == "SMOIS" || var_name == "SH2O" || var_name == "ZS" || var_name == "DZS") {
        // soil variables are staggered in z
        my_box.setType(amrex::IndexType(amrex::IntVect(0,0,1)));
    }
 
    amrex::Arena* Arena_Used = amrex::The_Arena();
#ifdef AMREX_USE_GPU
    // Make sure temp lives on CPU since nc_arrays lives on CPU only
    Arena_Used = amrex::The_Pinned_Arena();
#endif
    temp.resize(my_box,1, Arena_Used);
    amrex::Array4<DType> fab_arr = temp.array();
 
    int ioff = temp.box().smallEnd()[0];
    int joff = temp.box().smallEnd()[1];
    int kmax = temp.box().bigEnd()[2]; // highest z level to be read in
    //amrex::Print() << var_name << " domain khi, kmax, ns1 = " << khi << " " << kmax << " " << ns1 << std::endl;
 
    auto num_pts = in_box.numPts();
 
    for (int n(0); n < num_pts; ++n) {
        int k  = n / (ns2*ns3);
        if (k > kmax) continue;
        int j  = (n - k*(ns2*ns3)) / ns3 + joff;
        int i  = n - k*(ns2*ns3) - (j-joff) * ns3 + ioff;
        fab_arr(i,j,k,0) = static_cast<DType>(*(nc_arrays[iv].get_data()+n));
    }
}
 
/**
 * Function to read NetCDF variables and fill the corresponding Array4's
 *
 * @param domain Box specifying the domain covered by the NetCDF fields
 * @param fname Name of the NetCDF file to be read
 * @param nc_var_names Variable names in the NetCDF file
 * @param NC_dim_types NetCDF data dimension types
 * @param fab_vars Fab data we are to fill
 * @param success Success flags for each requested variable
 */
template<class FAB,typename DType>
void
BuildFABsFromNetCDFFile (const amrex::Box& domain,
                         const std::string &fname,
                         amrex::Vector<std::string> nc_var_names,
                         amrex::Vector<enum NC_Data_Dims_Type> NC_dim_types,
                         amrex::Vector<FAB*> fab_vars,
                         amrex::Vector<int>& success)
{
    int ioproc = amrex::ParallelDescriptor::IOProcessorNumber();  // I/O rank
 
    amrex::Vector<NDArray<float>> nc_arrays(nc_var_names.size());
 
    if (amrex::ParallelDescriptor::IOProcessor())
    {
        ReadNetCDFFile(fname, nc_var_names, nc_arrays, success);
    }
 
    amrex::ParallelDescriptor::Bcast(success.dataPtr(), success.size(), ioproc);
 
    for (int iv = 0; iv < nc_var_names.size(); iv++)
    {
        if (success[iv] == 1) {
            FAB tmp;
            if (amrex::ParallelDescriptor::IOProcessor()) {
                fill_fab_from_arrays<FAB,DType>(iv, domain, nc_arrays, nc_var_names[iv], NC_dim_types[iv], tmp);
            }
 
            int ncomp = tmp.nComp();
            amrex::Box box = tmp.box();
 
            amrex::ParallelDescriptor::Bcast(&box,   1, ioproc);
            amrex::ParallelDescriptor::Bcast(&ncomp, 1, ioproc);
 
            if (!amrex::ParallelDescriptor::IOProcessor()) {
#ifdef AMREX_USE_GPU
                tmp.resize(box,ncomp,amrex::The_Pinned_Arena());
#else
                tmp.resize(box,ncomp);
#endif
            }
 
            amrex::ParallelDescriptor::Bcast(tmp.dataPtr(), tmp.size(), ioproc);
 
            // Shift box by the domain lower corner
            amrex::Box  fab_bx = tmp.box();
            amrex::Dim3 dom_lb = lbound(domain);
            fab_bx += amrex::IntVect(dom_lb.x,dom_lb.y,dom_lb.z);
            // fab_vars points to data on device
            fab_vars[iv]->resize(fab_bx,1);
#ifdef AMREX_USE_GPU
            amrex::Gpu::copy(amrex::Gpu::hostToDevice,
                             tmp.dataPtr(), tmp.dataPtr() + tmp.size(),
                             fab_vars[iv]->dataPtr());
#else
            // Provided by BaseFab inheritance through FArrayBox
            fab_vars[iv]->copy(tmp,tmp.box(),0,fab_bx,0,1);
#endif
        } // success
    } // iv
}
#endif