Inputs

The GX input file

The main GX input file is parsed with toml. Input file names should be suffixed with .in, such as example.in. Such an input file can be run via

[/path/to/]gx example.in

This will generate an output file in NetCDF format called example.nc.

The toml standard allows one to group related input variables. There are multiple ways to specify such groupings. Since there are sample input files provided with GX, here we will pick one particular syntactical pattern. Users are free to use anything that is compatible with the toml standard.

Example input files can be found in the Getting started with GX pages, and in the benchmarks directory in the GX repository.

A typical input file will be of the form

debug = false

[Dimensions]
nx = ...
...

[Domain]
...

...

Most of the parameters belong to groups, e.g. [Dimensions] or [Domain].

In the following we describe each possible input parameter in each group. In practice, many of these parameters can be left unspecified so that default values are used.

debug is a special parameter that does not belong to a group, and must be specified at the top of the input file before any groups:

Group	Variable	Description	Default
none	debug	If true, print debug information to standard out	false

Dimensions

The [Dimensions] group controls the number of grid-points/spectral basis functions in each dimension, and the number of evolved kinetic species.

Group	Variable	Description	Default
[Dimensions]	nx	The number of real-space grid points in the x direction. Related to the number of de-aliased Fourier modes nkx via nkx = 1 + 2*(nx-1)/3. Recommended for nonlinear calculations (instead of nkx).
[Dimensions]	ny	The number of real-space grid points in the y direction. Related to the number of de-aliased Fourier modes nky via nky =  1 + (ny-1)/3. Recommended for nonlinear calculations (instead of nky).
[Dimensions]	nkx	The number of (de-aliased) Fourier modes in the x direction. Recommended for linear calculations (instead of nx).
[Dimensions]	nky	The number of (de-aliased) Fourier modes in the y direction. Recommended for linear calculations (instead of ny).
[Dimensions]	ntheta	The number of grid points used in the z direction.	32
[Dimensions]	nhermite	The number of Hermite basis functions used (\(v_\parallel\) resolution)	4
[Dimensions]	nlaguerre	The number of Laguerre basis functions used (\(\mu B\) resolution)	2
[Dimensions]	nspecies	The number of kinetic species used.	1
[Dimensions]	nperiod	The number of poloidal turns used. nperiod=1 recommended for nonlinear calculations.	1

Domain

The [Domain] group controls the physical extents of the simulation domain and the boundary conditions.

Group	Variable	Description	Default
[Domain]	y0	Controls box length in the binormal coordinate \(y\) via \(L_y = 2\pi \texttt{y0}\) (in units of \(\rho_\mathrm{ref}\)). Also controls the minimum \(k_y\), so that \(k_{y\,\mathrm{min}}\rho_\mathrm{ref} = 1/\texttt{y0}\).	10.0
[Domain]	jtwist	The twist-and-shift boundary condition is controlled by jtwist. This also effectively sets x0 via \(\texttt{x0} = \texttt{y0}\,\texttt{jtwist}/(2\pi\texttt{shat})\). Typically, if the magnetic shear \(\hat{s}\) is finite, you should set jtwist to be an integer close to \(2 \pi \hat{s}\), which will make \(\texttt{x0}\approx \texttt{y0}\) (the default behavior).	If finite magnetic shear: \(\texttt{round}(2\pi\texttt{shat})\) If zero magnetic shear: \(2\, \texttt{nx}\)
[Domain]	x0	Controls box length in the radial coordinate \(x\) via \(L_x = 2\pi \texttt{x0}\) (in units of \(\rho_\mathrm{ref}\)). Also controls the minimum \(k_x\), so that \(k_{x\,\mathrm{min}}\rho_\mathrm{ref} = 1/\texttt{x0}\). Typically jtwist should be set instead of x0 if the magnetic shear is finite.	If finite magnetic shear: \(\texttt{y0}\,\texttt{jtwist}/(2\pi\texttt{shat})\) If zero magnetic shear: \(\texttt{y0}\)
[Domain]	boundary	Controls the boundary condition in the \(z\) (parallel) direction. The following options are possible: - "linked": twist-and-shift BC, with generalization for non-axisymmetric geometry (Martin et al 2018). - "forced periodic" (or simply "periodic"): use periodic BCs with no cutting of flux tube. - "exact periodic": cut flux tube at a location where gds21 = 0, and then use periodic BCs (currently for VMEC geometry only). - "continuous drifts": cut flux tube at a location where gbdrift0 = 0, and then use (generalized) twist-and-shift BC (currently for VMEC geometry only). - "fix aspect": cut flux tube at a location where y0/x0 takes the desired value, and then use (generalized) twist-and-shift BC (VMEC geometry only).	“linked”
[Domain]	zp	Number of \(2\pi\) segments in the \(z\) (parallel) direction. Usually nperiod should be set instead.	\(2\,\texttt{nperiod}-1\)

Physics

Parameters that control physics options are specified in the [Physics] group:

Group	Variable	Description	Default
[Physics]	beta	This is the reference beta value, \(\beta_\mathrm{ref} = 8\pi n_\mathrm{ref} T_\mathrm{ref}/B^2\). Typically it would be approximately half of the total beta. If beta > 0.0 then electromagnetic terms will be used (depending on fapar and fbpar values); otherwise, if beta <= 0., it is ignored and the calculation is electrostatic.	0.0
[Physics]	nonlinear_mode	Set to true to include nonlinear terms in the equations.	false
[Physics]	fphi	Factor multiplying electrostatic potential \(\Phi\)	1.0
[Physics]	fapar	Factor multiplying electromagnetic vector potential \(A_\parallel\)	0.0
[Physics]	fbpar	Factor multiplying electromagnetic compressional fluctuation \(\delta B_\parallel\)	0.0

Time

Parameters that control the time-stepping are set in the [Time] group:

Group	Variable	Description	Default
[Time]	dt	The maximum timestep allowed. The actual timestep will be set by stability constraints.	0.05
[Time]	nstep	The number of timesteps to take. Set this or t_max to control the length of the simulation.
[Time]	t_max	End time of the simulation, in code units. Set this or nstep to control the length of the simulation.
[Time]	t_add	If restarting the simulation, run for an additional t_add time units.
[Time]	scheme	This string variable chooses the time-stepping scheme to be used. Choices are: "rk3": 3rd order Runge-Kutta (recommended) "rk4": 4th order Runge-Kutta "sspx3": 3rd order SSP Runge-Kutta with extended stability "k10": Ketcheson’s 10 stage, 4th order low-storage method. Useful for problems with memory constraints.	“rk3”
[Time]	stages	The number of Runge-Kutta stages to be used for certain time-stepping schemes. Not relevant for most choices of scheme.	10
[Time]	cfl	Safety cushion factor on timestep size. The timestep used will be the computed allowable timestep multiplied by cfl. If encountering numerical issues, decreasing cfl is one of the first things to try!	0.9

Initialization

The [Initialization] group controls the initial conditions.

Group	Variable	Description	Default
[Initialization]	init_field	The initial perturbation is applied to this component of the distribution function.	“density”
[Initialization]	init_amp	The amplitude of the initial perturbation.	1.0e-5
[Initialization]	ikpar_init	Parallel wavenumber of the initial perturbation	0
[Initialization]	init_electrons_only	Only apply initial perturbations to electrons (when using a kinetic electron species)	false
[Initialization]	random_init	Use completely random initial conditions (e.g. no mode structure in \(z\))	false
[Initialization]	gaussian_init	Use a gaussian initial condition in \(z\) with an envelope of \(a + b*sin(z-z0)\)	false
[Initialization]	gaussian_envelope_constant_coefficient	Coefficient \(a\) in the above expression for gaussian initial condition	1.0
[Initialization]	gaussian_envelope_sine_coefficient	Coefficient \(b\) in the above expression for gaussian initial condition	0.0
[Initialization]	gaussian_width	Width (in z) of the gaussian initial condition	0.5

Geometry

The [Geometry] group controls the simulation geometry.

Group	Variable	Description	Default
[Geometry]	geo_option	String specifying the geometry setup. Options are {"s-alpha", "miller", "vmec", "eik", "nc", "slab", "const-curv", "gs2_geo"}	“miller”

Each geo_option has some parameters that control the geometry specification. The following groups of parameters are the parameters that can/should be specified for a particular choice of geo_option. All parameters live in the [Geometry] block. Note that some parameters overlap between different geo_option’s.

geo_option = “miller”

This option specifies a local Miller equilibrium for a tokamak.

Group	Variable	Description	Default
[Geometry]	Rmaj	The ratio of the major radius at the center of the flux surface to the equilibrium-scale reference length, \(R/L_\mathrm{ref}\). The choice of Rmaj can effectively choose the definition of \(L_\mathrm{ref}\). Setting Rmaj = 1.0 effectively sets \(L_\mathrm{ref} = R\). Setting Rmaj to the aspect ratio \(R/a\) (with \(a\) the minor radius) effectively sets \(L_\mathrm{ref} = a\).	1.0
[Geometry]	qinp	The magnetic safety factor, \(q = (r/R)(B_t/B_p)\).	1.4
[Geometry]	shat	The global magnetic shear, \(\hat{s} = (r/q) dq/dr\).	0.8
[Geometry]	shift	This characterizes the Shafranov shift and is sometimes called alpha. It should normally be a non-negative number.	0.0
[Geometry]	rhoc	Flux surface label given by ratio of midplane diameter to the reference length, \(\rho = r/L_\mathrm{ref}\).
[Geometry]	R_geo	Major radius of magnetic field reference point, normalized to \(L_\mathrm{ref}\) (i.e. \(B_t(R_\mathrm{geo}) = B_\mathrm{ref}\)).
[Geometry]	akappa	Elongation of flux surface.
[Geometry]	akappri	Radial gradient of elongation of flux surface.
[Geometry]	tri	Triangularity of flux surface.
[Geometry]	tripri	Radial gradient of triangularity of flux surface.
[Geometry]	betaprim	Radial gradient of equilibrium pressure. Used in the calculation of the Shafranov shift.

geo_option = “vmec”

This option generates the geometry from a VMEC equilibrium output file in NetCDF format. This is typically used for stellarators. See also the boundary parameter in [Domain], where some options are only available for VMEC geometry.

Group	Variable	Description	Default
[Geometry]	vmec_file	(Path to) the VMEC equilibrium NetCDF output file.
[Geometry]	alpha	Field line label.	0.0
[Geometry]	npol	Number of poloidal turns. May be reduced based on boundary.	1.0
[Geometry]	desired_normalized_toroidal_flux or torflux	Flux surface label given by \(\rho = \sqrt{\Psi/\Psi_{LCFS}}\), where \(\Psi\) is the toroidal flux.	0.25
[Geometry]	vmec_surface_option	Controls how the flux surface is chosen. 0 = use exact radius requested. 1 = use nearest value of the VMEC half grid. 2 = use nearest value of the VMEC full grid.	0
[Geometry]	which_crossing	For boundary = "exact periodic", boundary = "continuous drifts", or boundary = "fix aspect", this controls which crossing of the relevant quantity to cut the flux tube at. Negative values count from the end of the flux tube.	-1
[Geometry]	verbose	Set to 1 to print lots of information from VMEC geometry module.	0

geo_option = “eik”

Read the geometry arrays from a text file in GS2’s eik.out format.

Group	Variable	Description	Default
[Geometry]	geo_file	(Path to) eik geometry file.	“eik.out”

geo_option = “nc”

Read the geometry arrays from a NetCDF file.

Group	Variable	Description	Default
[Geometry]	geo_file	(Path to) NetCDF geometry file.

geo_option = “s-alpha”, geo_option = “const-curv”

Group	Variable	Description	Default
[Geometry]	eps	Flux surface label given by the inverse aspect ratio of the surface in question, \(\epsilon = r/R\).	0.167
[Geometry]	Rmaj	The ratio of the major radius at the center of the flux surface to the equilibrium-scale reference length, \(R/L_\mathrm{ref}\). The choice of Rmaj can effectively choose the definition of \(L_\mathrm{ref}\). Setting Rmaj = 1.0 effectively sets \(L_\mathrm{ref} = R\). Setting Rmaj to the aspect ratio \(R/a\) (with \(a\) the minor radius) effectively sets \(L_\mathrm{ref} = a\).	1.0
[Geometry]	qinp	The magnetic safety factor, \(q = (r/R)(B_t/B_p)\).	1.4
[Geometry]	shat	The global magnetic shear, \(\hat{s} = (r/q) dq/dr\).	0.8
[Geometry]	shift	This characterizes the Shafranov shift and is sometimes called alpha. It should normally be a non-negative number.	0.0

geo_option = “gs2_geo”

This option calls GS2’s eiktest executable to run GS2’s geometry module directly. This is useful for generating geometry from a g-eqdsk equilibrium file, which is currently not natively supported in GX. This option requires separately building GS2’s eiktest and setting GS2_PATH in the Makefile. For parameter definitions, see the GS2 documentation, or see the comments at the top of src/geo/geometry.f90 in the GS2 source code.

Group	Variable	Description	Default
[Geometry]	rhoc	Value of flux surface label \(\rho\), depending on choice of irho	0.5
[Geometry]	irho	Choose flux surface label: case (1) :: sqrt(toroidal flux)/sqrt(toroidal flux of LCFS) case (2) :: diameter/(diameter of LCFS). recommended case (3) :: poloidal flux/(poloidal flux of LCFS)	2
[Geometry]	eqfile	(Path to) numerical equilibrium file to read
[Geometry]	iflux	Use iflux=1 to use a numerical equilibrium (EFIT, CHEASE, etc)	0
[Geometry]	geoType		0
[Geometry]	delrho		0.01
[Geometry]	bishop		0
[Geometry]	isym		0
[Geometry]	s_hat_input		1.0
[Geometry]	p_prime_input		-2.0
[Geometry]	invLp_input		5.0
[Geometry]	alpha_input		0.0
[Geometry]	efit_eq	Set true to use an EFIT (e.g. g-eqdsk) equilibrium.	false
[Geometry]	dfit_eq		false
[Geometry]	gen_eq		false
[Geometry]	ppl_eq		false
[Geometry]	local_eq		false
[Geometry]	idfit_eq		false
[Geometry]	chs_eq		false
[Geometry]	transp_eq		false
[Geometry]	gs2d_eq		false

Species

The [species] group specifies parameters like charge, mass, and gradients of each kinetic species. For each parameter, an array is provided with entries for each species. Note that only the first nspecies elements will be read. For example, a typical [species] group might look like

# it is okay to have extra species data here; only the first nspecies elements of each item are used
[species]
 z     = [ 1.0,      -1.0     ]         # charge (normalized to Z_ref)
 mass  = [ 1.0,       2.7e-4  ]         # mass (normalized to m_ref)
 dens  = [ 1.0,       1.0     ]         # density (normalized to dens_ref)
 temp  = [ 1.0,       1.0     ]         # temperature (normalized to T_ref)
 tprim = [ 2.49,      2.49    ]         # temperature gradient, L_ref/L_T
 fprim = [ 0.8,       0.8     ]         # density gradient, L_ref/L_n
 vnewk = [ 0.0,       0.0     ]         # collision frequency
 type  = [ "ion",  "electron" ]         # species type

If nspecies=1, only the first values of each table will be used (to set up the ion species). If nspecies=2 the electron data will be used as well.

Group	Variable	Description	Default
[species]	z	The charge (normalized to \(Z_\mathrm{ref}\))
[species]	mass	The mass (normalized to \(m_\mathrm{ref}\))
[species]	dens	The density (normalized to \(n_\mathrm{ref}\))
[species]	temp	The temperature (normalized to \(T_\mathrm{ref}\))	1.0
[species]	tprim	Temperature gradient, \(L_\mathrm{ref}/L_T\)
[species]	fprim	Density gradient, \(L_\mathrm{ref}/L_n\)
[species]	vnewk	The collision frequency	0.0
[species]	type	The type of species, such as "ion" or "electron"	“ion”

Boltzmann

The [Boltzmann] group sets up a Boltzmann species, which can be either electrons (e.g. for ITG calculations) or ions (e.g. for ETG calculations).

Group	Variable	Description	Default
[Boltzmann]	add_Boltzmann_species	If true, include a species with a Boltzmann response	false
[Boltzmann]	Boltzmann_type	Specify the Boltzmann species type. Choose either "electrons" or "ions".	“electrons”
[Boltzmann]	tau_fac	Set the value of \(\tau = T_\mathrm{ref}/T_\mathrm{Boltzmann}\) (which is usually \(\tau = T_\mathrm{kinetic}/T_\mathrm{Boltzmann}\)).	1.0

Dissipation

The [Dissipation] group controls numerical dissipation parameters, including (mostly experimental) closure models. For more details, see Numerical dissipation and Closures.

Group	Variable	Description	Default
[Dissipation]	hypercollisions	If true, use hypercollision model to provide hyper-dissipation at grid-scales in velocity space. For details, see Numerical dissipation.	false
[Dissipation]	nu_hyper_l	If hypercollisions=true, sets strength of Laguerre hypercollisions at grid-scales in \(\mu B\).	0.5
[Dissipation]	nu_hyper_m	If hypercollisions=true, sets strength of Hermite hypercollisions at grid-scales in \(v_\parallel\).	0.5
[Dissipation]	p_hyper_l	If hypercollisions=true, sets exponent of Laguerre hypercollisions.	6
[Dissipation]	p_hyper_m	If hypercollisions=true, sets exponent of Hermite hypercollisions.	6
[Dissipation]	hyper	If true, use a simple hyperdiffusivity model to provide hyper-dissipation at grid-scales in the perpendicular dimensions. Recommended only for nonlinear calculations. For details, see Numerical dissipation.	false
[Dissipation]	D_hyper	If hyper=true, sets strength of hyperdiffusivity	0.5
[Dissipation]	p_hyper	If hyper=true, sets exponent of hyperdiffusivity to 2*p_hyper.	2
[Dissipation]	HB_hyper	If true, use the Hammett-Belli hyperdiffusivity model to provide hyper-dissipation at grid-scales in the perpendicular dimensions. Recommended only for nonlinear calculations. For details, see Numerical dissipation.	false
[Dissipation]	D_HB	If HB_hyper=true, sets the strength of the H-B hyperdiffusivity model.	1.0
[Dissipation]	w_osc	If HB_hyper=true, sets the frequency parameter in the H-B model.	0.0
[Dissipation]	p_HB	If HB_hyper=true, sets the exponent for the H-B model, where 2 corresponds to the fourth power of k.	2
[Dissipation]	closure_model	Closure model to use. For options, see Closures.	“none”
[Dissipation]	smith_par_q	A parameter for closure_model = "smith_par".	3
[Dissipation]	smith_perp_q	A parameter for closure_model = "smith_perp".	3

Restart

The [Restart] group controls reading and writing of data for restarting (continuing) from previous runs. Warning: restart capability is currently limited. See this issue.

Group	Variable	Description	Default
[Restart]	restart	Set to true to continue the simulation from a previous run. The simulation will be initialized to the previous state by reading data from the file specified by restart_from_file.	false
[Restart]	save_for_restart	Set to true to write information needed for a future restart. File is written every nsave timesteps.	true
[Restart]	restart_to_file	Filename to write data needed for restarting the present run.	“[input_stem].restart.nc”
[Restart]	restart_from_file	Filename for a file written from a previous run, to be read and used to continue (restart) the previous run.	“[input_stem].restart.nc”
[Restart]	nsave	Restart data will be written every nsave steps.	max(1, \(\texttt{nstep}\)/10)
[Restart]	scale	Multiply all variables in the restart data by a factor of scale.	1.0

Diagnostics

The [Diagnostics] group controls the diagnostic quantities that are computed and written to the NetCDF output file. For more details about diagnostic quantities and options, see Diagnostics and the NetCDF file.

Group	Variable	Description	Default
[Diagnostics]	omega	Write instantaneous estimates of the complex frequency for each Fourier component of the electrostatic potential.	false
[Diagnostics]	free_energy	Write the total free energy (integrated over the phase-space domain and summed over species) as a function of time.	true
[Diagnostics]	fluxes	Write the turbulent fluxes for each species.	false
[Diagnostics]	fixed_amplitude	Periodically rescale amplitude of phi to avoid overflow. Only for linear calculations.	false
[Diagnostics]	all_zonal_scalars	Write quantities such as the RMS value of the zonal component of the ExB velocity as function of time. This is a shortcut for turning on all such writes, instead of specifying them individually (below).	false
[Diagnostics]	avg_zvE	Write the RMS value of the zonal component of ExB velocity as a function time.	false
[Diagnostics]	avg_zkvE	Write the RMS value of the zonal component of the shear of the ExB velocity as a function time.	false
[Diagnostics]	avg_zkden	Write the RMS value of the zonal component of the guiding center radial density gradient as a function of time.	false
[Diagnostics]	avg_zkUpar	Write the RMS value of the zonal component of the guiding center parallel velocity as a function of time.	false
[Diagnostics]	avg_zkTpar	Write the RMS value of the zonal component of the guiding center parallel temperature as a function of time.	false
[Diagnostics]	avg_zkTperp	Write the RMS value of the zonal component of the guiding center perpendicular temperature as a function of time.	false
[Diagnostics]	avg_zkqpar	Write the RMS value of the zonal component of the guiding center parallel-parallel heat flux as a function of time.	false
[Diagnostics]	all_zonal	Write quantities such as the zonal component of the ExB velocity as function of x and time. This is a shortcut for turning on all such writes, instead of specifying them individually (below).	false
[Diagnostics]	vE	Write the zonal component of ExB velocity as a function of x and time.	false
[Diagnostics]	kvE	Write the zonal component of the shear of the ExB velocity as a function of x and time.	false
[Diagnostics]	kden	Write the zonal component of the radial gradient of the guiding center density as a function of x and time.	false
[Diagnostics]	kUpar	Write the zonal component of the radial gradient of the guiding center parallel velocity as a function of x and time.	false
[Diagnostics]	kTpar	Write the zonal component of the radial gradient of the guiding center parallel temperature as a function of x and time.	false
[Diagnostics]	kTperp	Write the zonal component of the radial gradient of the guiding center perpendicular temperature as a function of x and time.	false
[Diagnostics]	kqpar	Write the zonal component of the radial gradient of the guiding center parallel-parallel heat flux as a function of x and time.	false
[Diagnostics]	all_non_zonal	Write quantities such as the non-zonal y-component of the ExB velocity as function of x and time. This is a shortcut for turning on all such writes, instead of specifying them individually (below).	false
[Diagnostics]	xyvEx	Write the x-component of the ExB velocity as a function of x, y, and time.	false
[Diagnostics]	xyvEy	Write the non-zonal y-component of the ExB velocity as a function of x, y, and time.	false
[Diagnostics]	xykvE	Write the non-zonal part of the shear of the y-component of the ExB velocity as a function of x and time.	false
[Diagnostics]	xyden	Write the non-zonal component of the guiding center density as a function of x and time.	false
[Diagnostics]	xyUpar	Write the non-zonal component of the guiding center parallel velocity as a function of x and time.	false
[Diagnostics]	xyTpar	Write the non-zonal component of the guiding center parallel temperature as a function of x and time.	false
[Diagnostics]	xyTperp	Write the non-zonal component of the guiding center perpendicular temperature as a function of x and time.	false
[Diagnostics]	xyqpar	Write the non-zonal component of the guiding center parallel-parallel heat flux as a function of x and time.	false

The [Wspectra] group controls writes of various slices of \(W_s(k_x,k_y,z, \ell, m) = |G_{\ell,m\,s}|^2\), the moment component of the free energy.

Group	Variable	Description	Default
[Wspectra]	species	W as a function of species	false
[Wspectra]	kx	W as a function of kx	false
[Wspectra]	ky	W as a function of ky	false
[Wspectra]	kz	W as a function of kz	false
[Wspectra]	z	W as a function of z	false
[Wspectra]	laguerre	W as a function of the Laguerre index	false
[Wspectra]	hermite	W as a function of the Hermite index	false
[Wspectra]	hermite_laguerre	W as a function of both Hermite and Laguerre indices	false
[Wspectra]	kperp	W as a function of the magnitude of kperp. Not yet implemented.	false
[Wspectra]	kxky	W as a function of the magnitude of kx and ky.	false

The [Pspectra] group controls writes of various slices of \(P_s(k_x,k_y,z) = [1-\Gamma_0(b_s)] |\Phi|^2\), the field component of the free energy.

Group	Variable	Description	Default
[Pspectra]	species	P as a function of species	false
[Pspectra]	kx	P as a function of kx	false
[Pspectra]	ky	P as a function of ky	false
[Pspectra]	kz	P as a function of kz	false
[Pspectra]	z	P as a function of z	false
[Pspectra]	kperp	P as a function of the magnitude of kperp. Not yet implemented.	false
[Pspectra]	kxky	P as a function of the magnitude of kx and ky.	false

The [Qspectra] group controls writes of various slices of \(Q_s(k_x,k_y,z)\), the heat flux.

Group	Variable	Description	Default
[Qspectra]	species	Q as a function of species	false
[Qspectra]	kx	Q as a function of kx	false
[Qspectra]	ky	Q as a function of ky	false
[Qspectra]	kz	Q as a function of kz	false
[Qspectra]	z	Q as a function of z	false
[Qspectra]	kperp	Q as a function of the magnitude of kperp. Not yet implemented.	false
[Qspectra]	kxky	Q as a function of the magnitude of kx and ky.	false

The [Gamspectra] group controls writes of various slices of \(\Gamma_s(k_x,k_y,z)\), the particle flux.

Group	Variable	Description	Default
[Gamspectra]	species	\(\Gamma\) as a function of species	false
[Gamspectra]	kx	\(\Gamma\) as a function of kx	false
[Gamspectra]	ky	\(\Gamma\) as a function of ky	false
[Gamspectra]	kz	\(\Gamma\) as a function of kz	false
[Gamspectra]	z	\(\Gamma\) as a function of z	false
[Gamspectra]	kperp	\(\Gamma\) as a function of the magnitude of kperp. Not yet implemented.	false
[Gamspectra]	kxky	\(\Gamma\) as a function of the magnitude of kx and ky.	false

Expert

The [Expert] group controls parameters reserved for expert users.

Group	Variable	Description	Default
[Expert]	i_share	An integer related to the shared memory block used for the inner loop of the linear solver.	8
[Expert]	nreal	Enforce the reality condition every nreal timesteps.	1
[Expert]	dealias_kz	If true, dealias in \(k_z\). Only available for boundary="periodic".	false
[Expert]	local_limit	If true, run calculation in local limit, where \(k_z\) is a scalar parameter given by \(k_z = 1.0/\texttt{zp}\).	false
[Expert]	init_single	Only initialize a single Fourier mode if true	false
[Expert]	ikx_single	Index of the kx mode to be initialized if init_single is true	0
[Expert]	iky_single	Index of the ky mode to be initialized if init_single is true	1
[Expert]	eqfix	Do not evolve some particular Fourier harmonic	false
[Expert]	ikx_fixed	Index of the kx mode to be fixed in time if eqfix is true	-1
[Expert]	iky_fixed	Index of the ky mode to be fixed in time if eqfix is true	-1
[Expert]	phi_ext	Value of phi to use for a Rosenbluth-Hinton test	0.0
[Expert]	source	Used to specify various kinds of tests	“default”
[Expert]	t0	The time at which to start changing tprim	-1.0
[Expert]	tf	The time at which to stop changing tprim	-1.0
[Expert]	tprim0	The value of tprim to start with (at time t0)	-1.0
[Expert]	tprimf	The value of tprim to end with (at time tf)	-1.0

Forcing

Add forcing with the [Forcing] group. Not generally implemented.

Group	Variable	Description	Default
[Forcing]	forcing_type	Picks among the forcing options	“Kz”
[Forcing]	stir_field	Determines which moment of the GK equation is forced	“density”
[Forcing]	forcing_amp	Amplitude of the forcing	1.0
[Forcing]	forcing_index	Index of the forcing	1
[Forcing]	no_fields	Turn off the field terms in the GK equation if this is true	false