API Reference

gauss_hermite(inputs::InputTJLF{T}) where T<:Real

parameters: inputs::InputTJLF{T} - InputTJLF struct constructed in tjlfreadinput.jl

outputs: OutputHermite(x,wx,h) - OutputHermite struct

description: computes abscisca's and weights for Gauss- Hermite integration adapted from Numerical Recipes in Fortran Pg.147 reversed order of roots so that x(m) is largest and x(1) is smallest only the positive roots are found and stored #————————————————————– initializes the hermite basis functions and ten point Gauss-Hermite integration with absissas x and weights w.

get_ky_spectrum(inputs::InputTJLF{T}, grad_r0::T)::Vector{T} where T<:Real

parameters: inputs::InputTJLF{T} - InputTJLF struct constructed in tjlfreadinput.jl gradr0::T - value from SaturationParameters struct from tjlfgeometry.jl

outputs: ky_spectrum::Vector{T} - array of floats that form the ky grid

description: the input file provides the type of kygrid to create (values 1 to 5) and this function creates it accordingly

get_ky_spectrum_size(nky::Int,kygrid_model::Int)::Int

parameters: nky::Int - nky from input file kygridmodel::Int - kygridmodel from input file

outputs: size of the ky_spectrum array

description: called before creation of InputTJLF struct to get the size of ky_spectrum

get_sat_params(inputs::InputTJLF{T}; ms::Int=128) where T<:Real

parameters: inputs::InputTJLF{T} - InputTJLF struct constructed in tjlfreadinput.jl

outputs: SaturationParameters{Float64}() - SaturationParameters struct calculated

description: compute the geometric coefficients on the x-grid

location: tjlf_geometry.jl

get_wavefunction(inputs::InputTJLF, satParams::SaturationParameters, field_weight_out::Array{ComplexF64,3})

Reconstruct the linear mode structure (wavefunction) along the extended ballooning angle from the Hermite-basis field weights produced by run (its field_weight_out).

parameters: inputs::InputTJLF - the input used for the run satParams::SaturationParameters - saturation/geometry params (get_sat_params) fieldweightout::Array{ComplexF64,3} - mode field weights [field, basis, mode] from run

outputs: plotfieldout - fields on the angle grid [mode, field, point] plotangleout - ballooning angle θ per grid point maxplot - number of angle-grid points nmodesout - number of modes returned

description: Sums the basis-j Hermite functions weighted by field_weight_out onto a fixed extended-angle grid, for each mode and each active field (electrostatic, plus USE_BPER/USE_BPAR magnetic components). Useful for inspecting mode localization and parity.

pick_device(mode::Symbol)

parameters: mode::Symbol - :cpu, :gpu, or :auto

outputs: device::Symbol - :cpu or :gpu

description: Determines the device to use based on the mode and CUDA availability.

sum_ky_spectrum(inputs::InputTJLF{T},satParams::SaturationParameters{T},gamma_matrix::Matrix{T},QL::Array{T,5})where T <: Real

parameters: inputs - InputTJLF struct constructed using the input.TGLF file gammamatrix - matrix of gamma (mode, ky) QLweights - split into separate types of QL weights (field, species, mode, ky, type) type: (particle, energy, torodial stress, parallel stress, exchange) (optional) - a lot of optional parameters that I don't use -DSUN

outputs: QLfluxout - flux integral of the QL weights (field, species, type)

takes in the input.tglf file, ky values, gammas, quasilinear weights, calls
intensity_sat() which returns the QL intensity values, then calls
flux_integrals() which numerically integrates the fluxes

tjlf_TM(inputs::InputTJLF{T},satParams::SaturationParameters{T},outputHermite::OutputHermite{T}) where T<:Real

parameters: inputs::InputTJLF{T} - InputTJLF struct constructed in tjlfreadinput.jl satParams::SaturationParameters{T} - SaturationParameters struct constructed in tjlfgeometry.jl outputHermite::OutputHermite{T} - OutputHermite struct constructed in tjlfhermite.jl

outputs (named tuple): QLweights - 5d array of QL weights (field, species, mode, ky, type), type: (particle, energy, torodial stress, parallel stress, exchange) firstPasseigenvalue - 3d array of eigenvalues (mode, ky, type), type: (gamma, frequency) secondPasseigenvalue - 3d array of second pass eigenvalues (mode, ky, type), type: (gamma, frequency) fieldweightout - 4d array of field weights (field, basis, mode, ky) phibarmatrix - 2d array of phibar values (mode, ky), only meaningful for SAT_RULE=0

description: Main transport model function. Calls linear TGLF over a spectrum of ky's and computes spectral integrals of field, intensity, and fluxes.

xgrid_functions_geo(inputs::InputTJLF{T}, satParams::SaturationParameters{T}, gamma_matrix::Matrix{T};small::T=0.00000001)

parameters: inputs::InputTJLF{T} - InputTJLF struct constructed in tjlfreadinput.jl satParams::SaturationParameters{T} - SaturationParameters struct constructed in tjlfgeometry.jl gammamatrix::Vector{T} - growth rate eigenvalues for each mode

outputs: kx0e - value of kx0e for tge given gamma value

description: calculate kx0_e (spectral shift) given the growthrate used for the second pass of TM

location: tjlf_geometry.jl

xgrid_functions_geo(inputs::InputTJLF{T}, satParams::SaturationParameters{T}, outHermite::OutputHermite{T}, ky::T, ky_index::Int; kx0_e::T=NaN, ms::Int=128)

parameters: inputs::InputTJLF{T} - InputTJLF struct constructed in tjlfreadinput.jl satParams::SaturationParameters{T} - SaturationParameters struct constructed in tjlfgeometry.jl outputHermite::OutputHermite{T} - OutputHermite struct constructed in tjlfhermite.jl ky::T - ky value kyindex::Int - index used for multithreading kx0e::T=NaN - spectral shift provided for second pass

outputs: OutputGeometry{Float64}() - OutputGeometry struct for different WIDTHS value

description: create the OutputGeometry struct for the specific WIDTHS value used to calculate Ave structs (tjlf_matrix.jl) used in eigenmatrix population

location: tjlf_geometry.jl