APIs

Batsrus data container, with Dim being the dimension of output.

BATSRUS output high-level struct.

Batsrus file head information.

Type for Batsrus file information.

BATSRUS output standalone header information.

Adjust 2D plot ranges.

Create buffer for x and w.

 convertIDLtoVTK(filename; gridType=1, verbose=false)

Convert 3D BATSRUS *.out to VTK. If filename does not end with "out", it tries to find the ".info" and ".tree" file with the same name tag and generates 3D unstructured VTU file.

Keywords

• gridType::Symbol: Type of target VTK grid (vti: image, vtr: rectilinear, vts: structured grid).

 convertTECtoVTU(file::AbstractString, outname="out")
 convertTECtoVTU(head, data, connectivity, outname="out")

Convert unstructured Tecplot data to VTK. Note that if using voxel type data in VTK, the connectivity sequence is different from Tecplot: the 3D connectivity sequence in Tecplot is the same as the hexahedron type in VTK, but different with the voxel type. The 2D connectivity sequence is the same as the quad type, but different with the pixel type. For example, in 3D the index conversion is:

# PLT to VTK voxel index_ = [1 2 4 3 5 6 8 7]
for i in 1:2
	connectivity = swaprows!(connectivity, 4*i-1, 4*i)
end

 create_pvd(filepattern)

Generate PVD file for a time series collection of VTK data.

Example

create_pvd("*.vtu)

cutdata(data, var; plotrange=[-Inf,Inf,-Inf,Inf], dir="x", sequence=1)

Get 2D plane cut in orientation dir for var out of 3D box data within plotrange. The returned 2D data lies in the sequence plane from - to + in dir.

 fillCellNeighbors!(batl, iCell_G, DiLevelNei_III, iNodeNei_III, nBlock_P)

Fill neighbor cell indexes for the given block. The faces, edges, and vertices are ordered from left (-) to right (+) in x-y-z sequentially.

Vertices: Edges: (10,11 ignored)

7 ----- 8        . --4-- .

• . - . 7 . 8 . 5 ––- 6 . . –3– . 12 . . . . . . . . . 3 ––- 4 9 . –2– . . - . - . 5 . 6 1 ––- 2 . –1– .

Only tested for 3D.

 fill_vector_from_scalars(bd::BATS, var)

Construct vector of var from its scalar components. Alternatively, check get_vectors for returning vector components as saparate arrays.

 find_grid_block(batl, xyz_D)

Return processor local block index that contains a point. Input location should be given in Cartesian coordinates.

Find neighbors for any node in the tree. Only for Cartesian now.

 find_tree_node(batl, Coord_D)

Find the node that contains a point. The point coordinates should be given in generalized coordinates normalized by the domain size.

Find variable index in the BATSRUS data.

Get cell connectivity list.

 getRotationMatrix(axis::AbstractVector, angle::Real) --> SMatrix{3,3}

Create a rotation matrix for rotating a 3D vector around a unit axis by an angle in radians. Reference: Rotation matrix from axis and angle

Example

using LinearAlgebra
v = [-0.5, 1.0, 1.0]
v̂ = normalize(v)
θ = deg2rad(-74)
R = getRotationMatrix(v̂, θ)

Return sibling index (1-8) for the given block node matrix.

 get_anisotropy(bd::BATS, species=0)

Calculate the pressure anisotropy for species, indexing from 0.

Return the convection electric field from PIC outputs.

Return the Hall electric field from PIC outputs.

 get_magnitude(bd::BATS, var)

Calculate the magnitude of vector var. See get_vectors for the options.

 get_magnitude2(bd::BATS, var)

Calculate the magnitude square of vector var. See get_vectors for the options.

Return mesh range of bd.

 get_timeseries(files::AbstractArray, loc; tstep = 1.0)

Extract plasma moments and EM field from PIC output files at loc with nearest neighbor. Currently only works for 2D outputs. If a single point variable is needed, see interp1d.

Return value range of var in bd.

 get_vectors(bd::BATS, var)

Return a tuple of vectors of var. var can be :B, :E, :U, :U0, or :U1.

Read ascii format coordinates and data values.

Read binary format coordinates and data values.

 getfilehead(fileID::IoStream, filelist::FileList) -> NameTuple

Obtain the header information from BATSRUS output file of type linked to fileID.

Input arguments

• fileID::IOStream: file identifier.
• filelist::FileList: file information.

 getfilesize(fileID::IOStream, lenstr::Int32, ::Val{FileType})

Return the size in bytes for one snapshot.

Obtain file type.

 getvar(bd::BATS, var::AbstractString) -> Array

Return variable data from string var. This is also supported via direct indexing,

Examples

bd["rho"]

Return view of variable var in bd.

Logical shifts as the Fortran instrinsic function.

 interp1d(bd::BATS, var::AbstractString, loc::AbstractVector{<:AbstractFloat})

Interpolate var at spatial point loc in bd.

 interp1d(bd::BATS, var::AbstractString, point1::Vector, point2::Vector)

Interpolate var along a line from point1 to point2 in bd.

 interp2d(bd::BATS, var::AbstractString, plotrange=[-Inf, Inf, -Inf, Inf],
	 plotinterval=Inf; kwargs...)

Return 2D interpolated slices of data var from bd. If plotrange is not set, output data resolution is the same as the original.

Keyword Arguments

• innermask=false: Whether to mask the inner boundary with NaN.
• rbody=1.0: Radius of the inner mask. Used when the rbody parameter is not found in the header.
• useMatplotlib=true: Whether to Matplotlib (faster) or NaturalNeighbours for scattered interpolation. If true, a linear interpolation is performed on a constructed triangle mesh.

Perform Triangle interpolation of 2D data W on grid X, Y.

 load(filename; npict=1, verbose=false)

Read BATSRUS output files. Stores the npict snapshot from an ascii or binary data file into the arrays of coordinates x and data w.

Return the axis range for 2D outputs. See interp2d.

Generating consistent 2D arrays for passing to plotting functions.

Return global block index for the node.

 order_children!(batl::Batl, iNode, iMorton::Int, iNodeMorton_I::Vector{Int32})

Recursively apply Morton ordering for nodes below a root block. Store result into iNodeMortonI and iMortonNodeA using the iMorton index.

 order_tree(batl)

Return maximum AMR level in the used block and the Morton curve order. Set iNodeMorton_I indirect index arrays according to

1. root node order
2. Morton ordering for each root node

Return BATL header from info file. Currently only designed for 2D and 3D.

Read information from log file.

 readtecdata(file; verbose=false)

Return header, data and connectivity from BATSRUS Tecplot outputs. Both 2D and 3D binary and ASCII formats are supported.

Examples

file = "3d_ascii.dat"
head, data, connectivity = readtecdata(file)

Return BATL tree structure.

 rotateTensorToVectorZ(tensor::AbstractMatrix, v::AbstractVector) -> SMatrix{3,3}

Rotate tensor with a rotation matrix that aligns the 3rd direction with vector, which is equivalent to change the basis from (i,j,k) to (i′,j′,k′) where k′ ∥ vector. Reference: Tensor rotation

 setunits(head, type; distance=1.0, mp=1.0, me=1.0)

Set the units for the output files. If type is given as "SI", "CGS", "NORMALIZED", "PIC", "PLANETARY", "SOLAR", set typeunit = type, otherwise try to guess from the fileheader. Based on typeunit set units for distance [xSI], time [tSI], density [rhoSI], pressure [pSI], magnetic field [bSI] and current density [jSI] in SI units. Distance unit [rplanet | rstar], ion and electron mass in [amu] can be set with optional distance, mp and me.

Also calculate convenient constants ti0, cs0 ... for typical formulas. This function is currently not used anywhere!

 showhead(file, head)

Displaying file header information.

 showhead(data)
 showhead(io, data)

Display file information of data.

 slice1d(bd, var, icut::Int=1, dir::Int=2)

Return view of variable var in bd along 1D slice. icut is the index along axis dir. dir == 1 means align with the 2nd (y) axis, dir == 2 means align with the 1st (x) axis.

Squeeze singleton dimensions for an array A.

subsurface(x, y, data, limits)
subsurface(x, y, u, v, limits)

Extract subset of 2D surface dataset in ndgrid format. See also: subvolume.

subvolume(x, y, z, data, limits)
subvolume(x, y, z, u, v, w, limits)

Extract subset of 3D dataset in ndgrid format. See also: subsurface.

Return matrix X with swapped rows i and j.

 macro bu_str(unit)

String macro to easily recall Batsrus units located in the UnitfulBatsrus package. Although all unit symbols in that package are suffixed with _bu, the suffix should not be used when using this macro. Note that what goes inside must be parsable as a valid Julia expression.

Example

julia> 1.0bu"u"
1.0 u
julia> 1.0bu"amucc"
1.0 amu/cc

Module for BATSRUS HDF5 file processing.

BATSRUS HDF5 file with uniform Cartesian mesh.

BATSRUS hdf5 file wrapper.

The data are stored in blocks, i.e., each field component is stored in a 4D array in the order (iblock, iz, iy, ix). This is a generic wrapper and does not assume grid type, i.e., uniform, stretched nonuniform, or AMR, etc. Classes to handle data with different grids can be derived from this class.

Return lower corner index.

 extract_var(file::BatsrusHDF5Uniform, var::String; kwargs...)

Extract variable var from HDF5 file.

Keywords

• xmin: minimum extracted coordinate in x.
• xmax: maximum extracted coordinate in x.
• stepx: extracted stride in x.
• ymin: minimum extracted coordinate in y.
• ymax: maximum extracted coordinate in y.
• stepy: extracted stride in y.
• zmin: minimum extracted coordinate in z.
• zmax: maximum extracted coordinate in z.
• stepz: extracted stride in z.
• verbose::Bool=true: display type and size information of output variable.

 global_slice_to_local_slice(file::BatsrusHDF5Uniform, dim, gslc, ib)

Convert global slice gslc to local slice lslc on a given block index ib.

 prep_extract(file::BatsrusHDF5Uniform, vmin=-Inf, vmax=Inf, step=1)

Get info for data extraction in 1D.

Keywords

• vmin, vmax: requested coordinate range (corner values).
• step: stride.

Returns:

• gslc: global slice.
• vmin_new, vmax_new: adjusted coordinate range (corner values).
• ibmin:ibmax: block range.

 prep_extract_per_block(file::BatsrusHDF5Uniform, dim, gslc, ib)

Get info for data extraction on a single block.

Arguments

• gslc: global slice from prep_extract.
• ib::Int: block index.

Returns

• lslc: range to be used on the current block.
• ix0:ix1: index range in the global array.

 prepslice(file::BatsrusHDF5Uniform; dim::Int, vmin, vmax, step=1)

Return range that covers [vmin, vmax) along dimension dim.

Returns

• slc_new: trimed slice. If the object's Nx==1, then 1:1 will be returned.
• xl_new: adjusted lower corner coordinate matching slc_new.start.
• xu_new: adjusted lower corner coordinate matching slc_new.stop.

 trimslice(start, stop, step, stop_max)

Set slice's start to be nonnegative and start/stop to be within bound. Reverse slicing is not handled.