NCFile.H File Reference

#include <sstream>
#include <string>
#include <ctime>
#include <atomic>
#include "AMReX_FArrayBox.H"
#include "AMReX_IArrayBox.H"
#include "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_BT_SN_WE , Time_SN_WE , SN_WE }

Functions
template<typename DType >
void	ReadNetCDFFile (const std::string &fname, amrex::Vector< std::string > names, amrex::Vector< NDArray< DType > > &arrays)
std::string	ReadNetCDFVarAttrStr (const std::string &fname, const std::string &var_name, const std::string &attr_name)
template<class FAB , typename DType >
void	fill_fab_from_arrays (int iv, 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)

Typedef Documentation

PlaneVector

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

Enumeration Type Documentation

NC_Data_Dims_Type

enum NC_Data_Dims_Type

strong

Enumerator
Time_BT_SN_WE
Time_SN_WE
SN_WE

                             {
    Time_BT_SN_WE,
    Time_SN_WE,
    SN_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
	)

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);
    }
 
    for (int iv = 0; iv < nc_var_names.size(); iv++)
    {
        FAB tmp;
        if (amrex::ParallelDescriptor::IOProcessor()) {
            fill_fab_from_arrays<FAB,DType>(iv, 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
    }
}

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fill_fab_from_arrays()

template<class FAB , typename DType >

void fill_fab_from_arrays	(	int	iv,
		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 nsx, nsy, nsz;
    if (NC_dim_type == NC_Data_Dims_Type::SN_WE) {
        nsz = 1;
        nsy = nc_arrays[iv].get_vshape()[0];
        nsx = nc_arrays[iv].get_vshape()[1];
        // amrex::Print() << "TYPE SN WE " << nsy << " " << nsx << std::endl;
    } else if (NC_dim_type == NC_Data_Dims_Type::Time_SN_WE) {
        nsz = 1;
        nsy = nc_arrays[iv].get_vshape()[1];
        nsx = nc_arrays[iv].get_vshape()[2];
        // amrex::Print() << "TYPE TIME SN WE " << nsy << " " << nsx << std::endl;
    } else if (NC_dim_type == NC_Data_Dims_Type::Time_BT_SN_WE) {
        nsz = nc_arrays[iv].get_vshape()[1];
        nsy = nc_arrays[iv].get_vshape()[2];
        nsx = nc_arrays[iv].get_vshape()[3];
        // amrex::Print() << "TYPE TIME BT SN WE " << nsx << " " << nsy << " " << nsz << std::endl;
    } else {
        amrex::Abort("Dont know this NC_Data_Dims_Type");
    }
 
    amrex::Box my_box;
 
    if (var_name == "u" || var_name == "ubar")
    {
        my_box.setSmall(amrex::IntVect(0,-1,0));
        my_box.setBig(amrex::IntVect(nsx-1,nsy-1,nsz-1));
        my_box.setType(amrex::IndexType(amrex::IntVect(1,0,0)));
    }
    else if (var_name == "v" || var_name == "vbar")
    {
        my_box.setSmall(amrex::IntVect(-1,0,0));
        my_box.setBig(amrex::IntVect(nsx-1,nsy-1,nsz-1));
        my_box.setType(amrex::IndexType(amrex::IntVect(0,1,0)));
    }
    else  // everything cell-centered -- these have one ghost cell
    {
        my_box.setSmall(amrex::IntVect(-1,-1,0));
        my_box.setBig(amrex::IntVect(nsx-2,nsy-2,nsz-1));
    }
 
    // amrex::Print() <<" NAME and BOX for this VAR " << var_name << " " << my_box << std::endl;
 
#ifdef AMREX_USE_GPU
    // Make sure temp lives on CPU since nc_arrays lives on CPU only
    temp.resize(my_box,1,amrex::The_Pinned_Arena());
#else
    temp.resize(my_box,1);
#endif
    amrex::Array4<DType> fab_arr = temp.array();
 
    int ioff = temp.box().smallEnd()[0];
    int joff = temp.box().smallEnd()[1];
 
    auto num_pts_in_box = my_box.numPts();
    auto num_pts_in_src = nsx*nsy*nsz;
    // amrex::Print() <<" NUM PTS IN BOX " << num_pts_in_box << std::endl;
    // amrex::Print() <<" NUM PTS IN SRC " << num_pts_in_src << std::endl;
    AMREX_ALWAYS_ASSERT(num_pts_in_box >= num_pts_in_src);
 
    for (int n(0); n < num_pts_in_src; ++n) {
        int nplane = nsx*nsy;
        int k  =  n / nplane;
        int j  = (n - k*nplane) / nsx + joff;
        int i  =  n - k*nplane - (j-joff) * nsx + 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_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) {
            // read the data from NetCDF file
            std::string vname_to_write = names[n];
            std::string vname_to_read  = names[n];
 
            // amrex::AllPrint() << "About to read " << vname_to_read
            //                   << " while filling the array for " << vname_to_write << std::endl;
 
            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);
 
            // 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 of the variable = (";
            // for (auto &dim:shape)
            //     amrex::Print() << dim << ", " ;
            // amrex::Print()  << ")" << std::endl;
 
            ncf.var(vname_to_read).get(dataPtr, start, shape);
        }
        ncf.close();
    }
}

Referenced by BuildFABsFromNetCDFFile().

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ReadNetCDFVarAttrStr()

std::string ReadNetCDFVarAttrStr	(	const std::string &	fname,
		const std::string &	var_name,
		const std::string &	attr_name
	)

Helper function for reading a single variable attribute

Parameters

fname	Name of NetCDF file
var_name	Name of variable
attr_name	Name of attribute to read

Returns

attribute value

{
    std::string attr_val;
    if (amrex::ParallelDescriptor::IOProcessor())
    {
        auto ncf = ncutils::NCFile::open(fname, NC_CLOBBER | NC_NETCDF4);
        attr_val = ncf.var(var_name).get_attr(attr_name);
        ncf.close();
    }
    return attr_val;
}

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