WriteBndryPlanes Class Reference

#include <ERF_WriteBndryPlanes.H>

Collaboration diagram for WriteBndryPlanes:

Public Member Functions
	WriteBndryPlanes (amrex::Vector< amrex::BoxArray > &grids, amrex::Vector< amrex::Geometry > &geom)
void	write_planes (int t_step, amrex::Real time, amrex::Vector< amrex::Vector< amrex::MultiFab >> &vars_new, bool is_moist)

Private Attributes
amrex::Box	target_box
	IO output box region. More...
amrex::Vector< amrex::Geometry > &	m_geom
	Geometry objects for all levels. More...
std::string	m_filename {""}
	File name for IO. More...
std::string	m_time_file {""}
	File name for Native time file. More...
amrex::Vector< std::string >	m_var_names
	Variables for IO. More...
amrex::Vector< amrex::Real >	m_in_times
	Timestep and times to be stored in time.dat. More...
amrex::Vector< int >	m_in_timesteps
int	m_in_rad = 1
	controls extents on native bndry output More...
const int	m_out_rad = 1
const int	m_extent_rad = 0

Static Private Attributes
static int	bndry_lev = 0

Detailed Description

Interface for writing boundary planes

This class performs the necessary file operations to write boundary planes

Constructor & Destructor Documentation

WriteBndryPlanes()

WriteBndryPlanes::WriteBndryPlanes ( amrex::Vector< amrex::BoxArray > &  grids, amrex::Vector< amrex::Geometry > &  geom  )

explicit

Constructor for the WriteBndryPlanes class for writing the contents of boundary planes to an output file

Parameters

grids	Vector of BoxArrays containing the grids at each level in the AMR
geom	Vector of Geometry containing the geometry at each level in the AMR

                                                            : m_geom(geom)
{
    ParmParse pp("erf");
 
    // Get the radius inside the domain
    pp.query("in_rad",m_in_rad);
 
    // User-specified region is given in physical coordinates, not index space
    std::vector<Real> box_lo(3), box_hi(3);
    pp.getarr("bndry_output_box_lo",box_lo,0,2);
    pp.getarr("bndry_output_box_hi",box_hi,0,2);
 
    // If the target area is contained at a finer level, use the finest data possible
    for (int ilev = 0; ilev < grids.size(); ilev++) {
 
        const Real* xLo   = m_geom[ilev].ProbLo();
        auto const dxi    = geom[ilev].InvCellSizeArray();
        const Box& domain = m_geom[ilev].Domain();
 
        // We create the smallest box that contains all of the cell centers
        // in the physical region specified
        int ilo = static_cast<int>(Math::floor((box_lo[0] - xLo[0]) * dxi[0])+Real(.5));
        int jlo = static_cast<int>(Math::floor((box_lo[1] - xLo[1]) * dxi[1])+Real(.5));
        int ihi = static_cast<int>(Math::floor((box_hi[0] - xLo[0]) * dxi[0])+Real(.5))-1;
        int jhi = static_cast<int>(Math::floor((box_hi[1] - xLo[1]) * dxi[1])+Real(.5))-1;
 
        // Map this to index space -- for now we do no interpolation
        target_box.setSmall(IntVect(ilo,jlo,0));
        target_box.setBig(IntVect(ihi,jhi,domain.bigEnd(2)));
 
        // Test if the target box at this level fits in the grids at this level
        Box gbx = target_box; gbx.grow(IntVect(1,1,0));
 
        // Ensure that the box is no larger than can fit in the (periodically grown) domain
        // at level 0
        if (ilev == 0) {
            Box per_grown_domain(domain);
            int growx = (geom[0].isPeriodic(0)) ? 1 : 0;
            int growy = (geom[0].isPeriodic(1)) ? 1 : 0;
            per_grown_domain.grow(IntVect(growx,growy,0));
            /*
            if (!per_grown_domain.contains(gbx))
                Error("WriteBndryPlanes: Requested box is too large to fill");
            */
        }
 
        if (grids[ilev].contains(gbx)) bndry_lev = ilev;
    }
 
    // The folder "m_filename" will contain the time series of data and the time.dat file
    pp.get("bndry_output_planes_file", m_filename);
 
    m_time_file = m_filename + "/time.dat";
 
    if (pp.contains("bndry_output_var_names"))
    {
        int num_vars = pp.countval("bndry_output_var_names");
        m_var_names.resize(num_vars);
        pp.queryarr("bndry_output_var_names",m_var_names,0,num_vars);
    }
}

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Member Function Documentation

write_planes()

void WriteBndryPlanes::write_planes	(	int	t_step,
		amrex::Real	time,
		amrex::Vector< amrex::Vector< amrex::MultiFab >> &	vars_new,
		bool	is_moist
	)

Function to write the specified grid data to an output file

Parameters

t_step	Timestep number
time	Current time
vars_new	Grid data for all variables across the AMR hierarchy

{
    BL_PROFILE("ERF::WriteBndryPlanes::write_planes");
 
    MultiFab& S    = vars_new[bndry_lev][Vars::cons];
    MultiFab& xvel = vars_new[bndry_lev][Vars::xvel];
    MultiFab& yvel = vars_new[bndry_lev][Vars::yvel];
    MultiFab& zvel = vars_new[bndry_lev][Vars::zvel];
 
    const std::string chkname =
        m_filename + Concatenate("/bndry_output", t_step);
 
    //Print() << "Writing boundary planes at time " << time << std::endl;
 
    const std::string level_prefix = "Level_";
    PreBuildDirectorHierarchy(chkname, level_prefix, 1, true);
 
    // note: by using the entire domain box we end up using 1 processor
    // to hold all boundaries
    BoxArray ba(target_box);
    DistributionMapping dm{ba};
 
    IntVect new_hi = target_box.bigEnd() - target_box.smallEnd();
    Box target_box_shifted(IntVect(0,0,0),new_hi);
    BoxArray ba_shifted(target_box_shifted);
 
    for (int i = 0; i < m_var_names.size(); i++)
    {
        std::string var_name = m_var_names[i];
        std::string filename = MultiFabFileFullPrefix(bndry_lev, chkname, level_prefix, var_name);
 
        int ncomp;
        if (var_name == "velocity") {
            ncomp = AMREX_SPACEDIM;
        } else {
            ncomp = 1;
        }
 
        BndryRegister bndry        (ba        , dm, m_in_rad, m_out_rad, m_extent_rad, ncomp);
        BndryRegister bndry_shifted(ba_shifted, dm, m_in_rad, m_out_rad, m_extent_rad, ncomp);
 
        int nghost = 0;
        if (var_name == "density")
        {
            bndry.copyFrom(S, nghost, Rho_comp, 0, ncomp, m_geom[bndry_lev].periodicity());
 
        } else if (var_name == "temperature") {
            MultiFab Temp(S.boxArray(),S.DistributionMap(),ncomp,0);
            for (MFIter mfi(Temp, TilingIfNotGPU()); mfi.isValid(); ++mfi)
            {
                const Box& bx = mfi.tilebox();
                if (is_moist) {
                    // NOTE: we send in S[mfi] where we should send in (*z_phys_cc[lev])[mfi] because we know this routine doesn't use it
                    derived::erf_dermoisttemp(bx, Temp[mfi], 0, 1, S[mfi], S[mfi], m_geom[bndry_lev], time, nullptr, bndry_lev);
                } else {
                    // NOTE: we send in S[mfi] where we should send in (*z_phys_cc[lev])[mfi] because we know this routine doesn't use it
                    derived::erf_dertemp(bx, Temp[mfi], 0, 1, S[mfi], S[mfi], m_geom[bndry_lev], time, nullptr, bndry_lev);
                }
            }
            bndry.copyFrom(Temp, nghost, 0, 0, ncomp, m_geom[bndry_lev].periodicity());
        } else if (var_name == "theta") {
            MultiFab Temp(S.boxArray(),S.DistributionMap(),ncomp,0);
            for (MFIter mfi(Temp, TilingIfNotGPU()); mfi.isValid(); ++mfi)
            {
                const Box& bx = mfi.tilebox();
                derived::erf_derrhodivide(bx, Temp[mfi], S[mfi], RhoTheta_comp);
            }
            bndry.copyFrom(Temp, nghost, 0, 0, ncomp, m_geom[bndry_lev].periodicity());
        } else if (var_name == "scalar") {
            MultiFab Temp(S.boxArray(),S.DistributionMap(),ncomp,0);
            for (MFIter mfi(Temp, TilingIfNotGPU()); mfi.isValid(); ++mfi)
            {
                const Box& bx = mfi.tilebox();
                derived::erf_derrhodivide(bx, Temp[mfi], S[mfi], RhoScalar_comp);
            }
            bndry.copyFrom(Temp, nghost, 0, 0, ncomp, m_geom[bndry_lev].periodicity());
        } else if (var_name == "ke") {
            MultiFab Temp(S.boxArray(),S.DistributionMap(),ncomp,0);
            for (MFIter mfi(Temp, TilingIfNotGPU()); mfi.isValid(); ++mfi)
            {
                const Box& bx = mfi.tilebox();
                derived::erf_derrhodivide(bx, Temp[mfi], S[mfi], RhoKE_comp);
            }
            bndry.copyFrom(Temp, nghost, 0, 0, ncomp, m_geom[bndry_lev].periodicity());
        } else if (var_name == "qv") {
            MultiFab Temp(S.boxArray(),S.DistributionMap(),ncomp,0);
            if (S.nComp() > RhoQ2_comp) {
                for (MFIter mfi(Temp, TilingIfNotGPU()); mfi.isValid(); ++mfi)
                {
                    const Box& bx = mfi.tilebox();
                    derived::erf_derrhodivide(bx, Temp[mfi], S[mfi], RhoQ1_comp);
                }
            } else {
                Temp.setVal(0.);
            }
            bndry.copyFrom(Temp, nghost, 0, 0, ncomp, m_geom[bndry_lev].periodicity());
        } else if (var_name == "qc") {
            MultiFab Temp(S.boxArray(),S.DistributionMap(),ncomp,0);
            if (S.nComp() > RhoQ2_comp) {
                for (MFIter mfi(Temp, TilingIfNotGPU()); mfi.isValid(); ++mfi)
                {
                    const Box& bx = mfi.tilebox();
                    derived::erf_derrhodivide(bx, Temp[mfi], S[mfi], RhoQ2_comp);
                }
            } else {
                Temp.setVal(0.);
            }
            bndry.copyFrom(Temp, nghost, 0, 0, ncomp, m_geom[bndry_lev].periodicity());
        } else if (var_name == "velocity") {
            MultiFab Vel(S.boxArray(), S.DistributionMap(), 3, m_out_rad);
            average_face_to_cellcenter(Vel,0,Array<const MultiFab*,3>{&xvel,&yvel,&zvel});
            bndry.copyFrom(Vel, nghost, 0, 0, ncomp, m_geom[bndry_lev].periodicity());
        } else {
            //Print() << "Trying to write planar output for " << var_name << std::endl;
            Error("Don't know how to output this variable");
        }
 
        for (OrientationIter oit; oit != nullptr; ++oit) {
            auto ori = oit();
            if (ori.coordDir() < 2) {
                std::string facename = Concatenate(filename + '_', ori, 1);
                br_shift(oit, bndry, bndry_shifted);
                bndry_shifted[ori].write(facename);
            }
        }
 
    } // loop over num_vars
 
    // Writing time.dat
    if (ParallelDescriptor::IOProcessor()) {
        std::ofstream oftime(m_time_file, std::ios::out | std::ios::app);
        oftime << std::setprecision(17) << t_step << ' ' << time << '\n';
        oftime.close();
    }
}

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Member Data Documentation

bndry_lev

int WriteBndryPlanes::bndry_lev = 0

staticprivate

Referenced by write_planes(), and WriteBndryPlanes().

m_extent_rad

const int WriteBndryPlanes::m_extent_rad = 0

private

Referenced by write_planes().

m_filename

std::string WriteBndryPlanes::m_filename {""}

private

File name for IO.

Referenced by write_planes(), and WriteBndryPlanes().

m_geom

amrex::Vector<amrex::Geometry>& WriteBndryPlanes::m_geom

private

Geometry objects for all levels.

Referenced by write_planes(), and WriteBndryPlanes().

m_in_rad

int WriteBndryPlanes::m_in_rad = 1

private

controls extents on native bndry output

Referenced by write_planes(), and WriteBndryPlanes().

m_in_times

amrex::Vector<amrex::Real> WriteBndryPlanes::m_in_times

private

Timestep and times to be stored in time.dat.

m_in_timesteps

amrex::Vector<int> WriteBndryPlanes::m_in_timesteps

private

m_out_rad

const int WriteBndryPlanes::m_out_rad = 1

private

Referenced by write_planes().

m_time_file

std::string WriteBndryPlanes::m_time_file {""}

private

File name for Native time file.

Referenced by write_planes(), and WriteBndryPlanes().

m_var_names

amrex::Vector<std::string> WriteBndryPlanes::m_var_names

private

Variables for IO.

Referenced by write_planes(), and WriteBndryPlanes().

target_box

amrex::Box WriteBndryPlanes::target_box

private

IO output box region.

Referenced by write_planes(), and WriteBndryPlanes().

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The documentation for this class was generated from the following files:

• Source/IO/ERF_WriteBndryPlanes.H
• Source/IO/ERF_WriteBndryPlanes.cpp