ERF_NCWpsFile.H File Reference

#include <sstream>
#include <string>
#include <atomic>
#include "AMReX_FArrayBox.H"
#include "AMReX_IArrayBox.H"
#include "ERF_EpochTime.H"
#include "ERF_NCInterface.H"

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Classes
struct	NDArray< DataType >

Typedefs
using	PlaneVector = amrex::Vector< amrex::FArrayBox >

Enumerations
enum class	NC_Data_Dims_Type {   Time_SL_SN_WE , Time_BT_SN_WE , Time_SN_WE , Time_BT ,   Time_SL , Time , Time_BdyWidth_BT_SN , Time_BdyWidth_BT_WE ,   Time_BdyWidth_SN , Time_BdyWidth_WE }

Functions
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)
template<typename DType >
void	ReadNetCDFFile (const std::string &fname, amrex::Vector< std::string > names, amrex::Vector< NDArray< DType > > &arrays, amrex::Vector< int > &success)
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)
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)

Typedef Documentation

PlaneVector

using PlaneVector = amrex::Vector<amrex::FArrayBox>

Enumeration Type Documentation

NC_Data_Dims_Type

enum NC_Data_Dims_Type

strong

Enumerator
Time_SL_SN_WE
Time_BT_SN_WE
Time_SN_WE
Time_BT
Time_SL
Time
Time_BdyWidth_BT_SN
Time_BdyWidth_BT_WE
Time_BdyWidth_SN
Time_BdyWidth_WE

                             {
    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
};

Function Documentation

BuildFABsFromNetCDFFile()

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
	)

Function to read NetCDF variables and fill the corresponding Array4's

Parameters

fname	Name of the NetCDF file to be read
nc_var_names	Variable names in the NetCDF file
NC_dim_types	NetCDF data dimension types
fab_vars	Fab data we are to fill

{
    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
}

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BuildFABsFromWRFBdyFile()

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
	)

fill_fab_from_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
	)

Helper function for reading data from NetCDF file into a provided FAB.

Parameters

iv	Index for which variable we are going to fill
nc_arrays	Arrays of data from NetCDF file
var_name	Variable name
NC_dim_type	Dimension type for the variable as stored in the NetCDF file
temp	FAB where we store the variable data from the NetCDF Arrays

{
    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));
    }
}

ReadNetCDFFile()

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();
    }
}

Referenced by BuildFABsFromNetCDFFile().

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ReadTimeSliceFromNetCDFFile()

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();
    }
}

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