cgs_to_SI_conversion_factors

Factors for converting some physical quantities from cgs-units to SI-units.

primary_vars

The primary variables and their order of storage for primary variables in a Bifrost .snap binary file.

BifrostExperiment(
    expname::String="none",
    expdir::String=pwd()
    ;
    mesh_file=nothing
    )

A struct for your Bifrost-experiment.

Fields:

    expname         ::String
    expdir          ::String
    snaps           ::Vector{Int64}
    snapsize        ::Tuple{Int64, Int64, Int64}
    num_snaps       ::Int64
    num_primary_vars::Int64

    BifrostMesh

Stores Bifrost grid information in struct

Base.display(xp::BifrostExperiment)

Prints information about the BifrostExperiment.

addtokwargs(;kwargs...)

Add keyword-arguments to your Base.Pairs of kwargs.

code_to_cgs(
    variable::String,
    params  ::Dict{String,String},
)

Conversion factor of variable from code units to cgs units.

convert_timeunits!(
t     ::AbstractArray,
params::Dict{String,String}
)     ::Float64

Converts snapshot time to seconds

convert_units(
    data    ::AbstractArray,
    variable::String,
    params  ::Dict{String,String},
    units   ::String,
    )

Convert the data from code units to cgs or SI. Conversion factor depends on variable and snapshot params.

dxdn(
	arr::Array{T,3},
	dz::Vector{T}, 
	periodic::Bool=false, 
	order::Int=6
	)

Computes the spatial derivative in the x-direction of every entry in arr shifted a half grid point downwards. Defaults to the 6th order accurate Bifrost derivative with order=6, optional 2nd order accurate derivative with keyword order=2

dxup(
	arr::Array{T,3},
	dz::Vector{T}, 
	periodic::Bool=false, 
	order::Int=6
	)

Computes the spatial derivative in the x-direction of every entry in arr shifted a half grid point upwards. Defaults to the 6th order accurate Bifrost derivative with order=6, optional 2nd order accurate derivative with keyword order=2

dydn(
	arr::Array{T,3},
	dz::Vector{T}, 
	periodic::Bool=false, 
	order::Int=6
	)

Computes the spatial derivative in the y-direction of every entry in arr shifted a half grid point downwards. Defaults to the 6th order accurate Bifrost derivative with order=6, optional 2nd order accurate derivative with keyword order=2

dyup(
	arr::Array{T,3},
	dz::Vector{T}, 
	periodic::Bool=false, 
	order::Int=6
	)

Computes the spatial derivative in the y-direction of every entry in arr shifted a half grid point upwards. Defaults to the 6th order accurate Bifrost derivative with order=6, optional 2nd order accurate derivative with keyword order=2

dzdn(
	arr::Array{T,3},
	dz::Vector{T}, 
	periodic::Bool=false, 
	order::Int=6
	)

Computes the spatial derivative in the z-direction of every entry in arr shifted a half grid point downwards. Defaults to the 6th order accurate Bifrost derivative with order=6, optional 2nd order accurate derivative with keyword order=2

dzup(
	arr::Array{T,3},
	dz::Vector{T}, 
	periodic::Bool=false, 
	order::Int=6
	)

Computes the spatial derivative in the z-direction of every entry in arr shifted a half grid point upwards. Defaults to the 6th order accurate Bifrost derivative with order=6, optional 2nd order accurate derivative with keyword order=2

function get_and_destagger_var(expname::String,
    filename::String,
    params::Dict{String,String},
    varnr::Integer,
    ;
    destaggeroperation::Function,
    units::String="none",
    periodic::Bool=false,
    order::Int=6,
    slicex::AbstractVector{<:Integer}=Int[],
    slicey::AbstractVector{<:Integer}=Int[],
    slicez::AbstractVector{<:Integer}=Int[],
    kwargs...
    )

Function to load a staggered variable and interpolate it to cell center. The staggered variables that typically need to be interpolated are the velocity and magnetic field components. Normally you need to use destaggeroperation=zup for vz and bz with periodic=false, and destaggeroperation=xup for vx and bx with periodic=true (same for y direction).

get_aux(
    file_name::String,
    params   ::Dict{String,String}
)

Reads Bifrost *.aux binary file using memory-mapping. The returned auxdata array will have dimensions (mx,my,mz,nvars) where nvars is the number of aux-variables. Assumes single floating point precision by default.

get_axes(
    xp::BifrostExperiment
    ;
    units="code"
    )

Return a tuple containing the axis of the BifrostExperiment in the desired units.

get_basename(
    expname ::String,
    snap    ::Union{<:Integer, AbstractVector{<:Integer}},
    expdir  ::String,
    )

Return the basename of snapshots in the experiment expname, located in the directory expdir. Also return the filename (withou file extension) of the first snapshot of the experiment.

function get_electron_density(
    xp::BifrostExperiment,
    snap::Integer,
    kwargs...)

Function to calculate the electron density from a snapshot snap. Supports slicing. Gas density rho and internal energy e are optional arguments and can be passed (but they MUST be in cgs units). If these quantities already exist, passing them will speed up the calculation of electron density.

kwargs: units::String="si", slicex::AbstractVector{<:Integer}=Int[], slicey::AbstractVector{<:Integer}=Int[], slicez::AbstractVector{<:Integer}=Int[], rho::Array{AbstractFloat,3}=Float32[;;;], e::Array{AbstractFloat,3}=Float32[;;;], tabfile::String="tabparam.in"

function get_electron_density(
    expname::String,
    snap::Integer,
    expdir::String;
    units::String="si",
    slicex::AbstractVector{<:Integer}=Int[],
    slicey::AbstractVector{<:Integer}=Int[],
    slicez::AbstractVector{<:Integer}=Int[],
    rho::Array{T,3}=Float32[;;;],
    e::Array{T,3}=Float32[;;;],
    tabfile::String="tabparam.in"
    ) where {T<:AbstractFloat}

get_numvars(
    params::Dict{String,String},
)

Returns number of primary variables and number of auxiliary variables, given the snapshot-parameters.

get_snap(
    expname::String,
    snap   ::Int,
    expdir ::String,
    )

Reads Bifrost *.snap binary file as an Array in dimension: (mx,my,mz,nvar). Takes experiment name, experiment directory, and snap number as arguments. Returns snapdata (the data) and params (the snap parameters). Assumes single floating point precision by default.

Variables of snapdata:

    snapdata[:,:,:,1] : r, density
    snapdata[:,:,:,2] : px, x-component of momentum
    snapdata[:,:,:,3] : py, y-component of momentum
    snapdata[:,:,:,4] : pz, z-component of momentum
    snapdata[:,:,:,5] : e, energy

    if params["do_mhd"] == 1 # numvars = 8, otherwise numvars = 5
        snapdata[:,:,:,6] : bx, x-component of magnetic field
        snapdata[:,:,:,7] : by, y-component of magnetic field
        snapdata[:,:,:,8] : bz, z-component of magnetic field

Warning: variables in code units.ts

get_snap(
    file_name::String,
    params   ::Dict{String,String}
    )

get_snap_numbers(
    expdir::String,
    expname::String="none"
    ;
    findall::Bool=false,
    filenames::Vector{String}=String[]
    )

Finds all files in the format 'expnameXXX.snap' in the experiment directory `expdir, and returns a vector of the snapshots XXX. Ifexpname` is not given, is is assumed that the directory of the simulation matches the experiment name.

get_snapsize(
    mesh::BifrostMesh,
)

Returns snapsize (mx, my, mz) given a Bifrost-mesh.

get_snapsize(
    params::Dict{String,String},
)

Returns snapsize (mx, my, mz) given the snapshot-parameters.

get_snapsize_and_numvars(
    params::Dict{String,String},
)

Returns snapsize (mx, my, mz), number of primary variables and number of auxiliary variables, given the snapshot-parameters.

get_var(
    xp::BifrostExperiment,
    snap::Union{<:Integer, AbstractVector{<:Integer}},
    variable::String,
    args...
    ;
    kwargs...
    )

Load a variable from one or multiple snapshots of xp.

Available variables

The primary variables:

• "r": density
• "px": x-component of momentum
• "py": y-component of momentum
• "pz": z-component of momentum
• "e": energy

if params["do_mhd"] == true

• "bx": x-component of magnetic field
• "by": y-component of magnetic field
• "bz": z-component of magnetic field

auxilliary variables (variables in params["aux"]):

• "p": pressure
• "tg": gas temperature ...

Optional keyword-arguments

Converts variables to "si" or "cgs" units: units="si" or units="cgs".

To load a slice of the variable, give e.g. slicex=[32, 410] or slicey=40:90

Example usage:

exp_name = "cb24oi"
exp_dir = "/mn/stornext/d21/RoCS/matsc/3d/run/cb24oi"
snap = 700

xp = BifrostExperiment(expname, expdir)

# Load pressude for the full cube in si units
pressure = get_var(xp, snap, "p"; units="si")

# Load gas density in a slize along the xy-plane in cgs units
rho = get_var(xp, snap, "r"; units="cgs", slicez=[100])

get_var(
    filename       ::String,
    params         ::Dict{String,String},
    varnr          ::Integer,
    precision      ::DataType=Float32;
    slicex         ::AbstractVector{<:Integer}=Int[],
    slicey         ::AbstractVector{<:Integer}=Int[],
    slicez         ::AbstractVector{<:Integer}=Int[]
    )

Load variable nr. varnr from filename. The variable could be either primary or auxiliary. Slicing the snapshot is optional. Assumes single precision snapshot by default.

get_var(
    expname ::String,
    snap    ::Union{<:Integer, AbstractVector{<:Integer}},
    expdir  ::String,
    variable::String,
    args...
    ;
    kwargs...
)

Load a variable from one or multiple snapshots of a Bifrost experiment with experiment directory expdir and experiment name expname.

get_variable_offset_in_file(
    precision::DataType,
    snapsize::Tuple{Integer, Integer, Integer},
    varnr   ::Integer
    )

Given the precision and size of a snapshot, find the offset for reading the variable with index varnr directly from file. Offset given in number of bytes.

get_varnr_and_file_suffix(
    params::Dict{String,String},
    variable::String
    )

Given the snapshot params and desired variable, return its index in the binary file, as well as the suffix of this file. (A format string where the snapshot number is to be inserted).

read_params(xp::BifrostExperiment, snap::Integer)

read_params(expname::String, snap::Integer, expdir::String)

read_params(file_name::String)

Reads and returns parameters params of a Bifrost simulation snapshot given the path file_name to the simulation snapshot. The input file should have the format 'name_xxx.idl' where 'name' is the simulation name and 'xxx' is the snapshot number

rotate(
    data         ::AbstractArray,
    variable     ::String,
    rotation_axis::String,
    )

Rotate the data about an rotation_axis.

function squeeze(a::AbstractArray)

Drop singleton dimensions of array a

function xdn(
    arr::Array{T,3},
    periodic::Bool=true,
    order::Int=6
) where {T<:AbstractFloat}

Stagger operation on arr by a 5th order polynomial interpolation, shifting the variable half a grid point downwards in the x-direction

function xup(
    arr::Array{T,3},
    periodic::Bool=true,
    order::Int=6
) where {T<:AbstractFloat}

Stagger operation on arr by a 5th order polynomial interpolation, shifting the variable half a grid point upwards in the x-direction

xupyup(data, args...)

For destagering variables at cell edges, in particular the z-axis.

function ydn(
    arr::Array{T,3},
    periodic::Bool=true,
    order::Int=6
) where {T<:AbstractFloat}

Stagger operation on arr by a 5th order polynomial interpolation, shifting the variable half a grid point downwards in the y-direction

function yup(
    arr::Array{T,3},
    periodic::Bool=true,
    order::Int=6
) where {T<:AbstractFloat}

Stagger operation on arr by a 5th order polynomial interpolation, shifting the variable half a grid point upwards in the y-direction

yupzup(data, args...)

For destagering variables at cell edges, in particular the x-axis.

function zdn(
    arr::Array{T,3},
    periodic::Bool=true,
    order::Int=6
) where {T<:AbstractFloat}

Stagger operation on arr by a 5th order polynomial interpolation, shifting the variable half a grid point downwards in the z-direction

function zup(
    arr::Array{T,3},
    periodic::Bool=true,
    order::Int=6
) where {T<:AbstractFloat}

Stagger operation on arr by a 5th order polynomial interpolation, shifting the variable half a grid point upwards in the z-direction

zupxup(data, args...)

For destagering variables at cell edges, in particular the y-axis.