Initialisation Options

GS2 has a lot of possible options for the initial condition. Of these, only a few are usually used: these are the typical and restarting

Typical options

These options are the most useful for ordinary GS2 simulations:

• "default": Gaussian in $\theta$. See ginit_default. Input parameters:

  • Amplitude: phiinit
  • Width in $\theta$: width0
  • Parity: chop_side and left

• "default_odd": Guassian in $\theta$ multiplied by $\sin(\theta - \theta_0)$. See ginit_default_odd. Input parameters:

  • Amplitude: phiinit
  • Width in $\theta$: width0
  • Parity: chop_side and left

• "noise": Noise along field line: each mode is given a random amplitude between zero and one. The recommended choice for nonlinear runs. See ginit_noise. Input parameters:

  • Amplitude: phiinit
  • Zonal flow factor: zf_init
  • Use a fixed set of random numbers: constant_random_flag
  • Continuity in parallel direction: clean_init
  • Single $k_x$ mode: ikx_init
  • Parity: chop_side and left
  • Seed for random numbers: seed

• "single_parallel_mode": Initialise only with a single parallel mode $k_\Vert$ specified by either ikpar_init for periodic boundary conditions or kpar_init for linked boundary conditions. Only makes sense for linear calculations. See ginit_single_parallel_mode

Less-usual options

There are many more initialisation options for GS2, although the majority are unmaintained and are specific to the studies they were originally written for. Unfortunately, many are also undocumented, so it is difficult to say precisely what they do

• "alf": Ion distribution function proportional to $v_\Vert \sin(\theta)$; do not use.
• "all_modes_equal": Initialise with every single parallel and perpendicular mode given the same amplitude. Intended for linear calculations
• "cgyro": CGYRO-like initialisation, constant amplitude for $k_y \ne 0$ and zero amplitude for $k_y == 0$ (see ginit_cgyro for details).
• "cont": Restart, using current value of g in memory; unsupported, do not use.
• "convect": Unsupported; do not use. Controlled by k0.

• "gs": Randomly phased $k_\Vert = 1$ sines and cosines in density, parallel velocity, and parallel and perpendicular temperatures. Controlled by:

  • Overall amplitude: phiinit
  • Amplitude of real and imaginary parts of $\phi$: refac, imfac
  • Density perturbation: den1
  • Parallel velocity perturbation: upar1
  • Parallel temperature perturbation: tpar1
  • Perpendicular temperature perturbation: tperp1

• "harris": Controlled by k0. Unsupported; do not use.

• "kpar": Initial perturbation in fields of form $x_0 + x_1 \cos(\theta) + x_2 \cos(2 \theta)$, except for parallel velocity which uses is 90 degrees out of phase and uses $\sin$. Density, parallel velocity, and perpendicular and parallel temperatures can all be controlled independently. Controlled by:

  • Overall amplitude: phiinit
  • Amplitude of real and imaginary parts of $\phi$: refac, imfac
  • Gaussian envelope width in $\theta$: width0
  • Density perturbation: den0, den1, den2
  • Parallel velocity perturbation: upar0, upar1, upar2
  • Parallel temperature perturbation: tpar0, tpar1, tpar2
  • Perpendicular temperature perturbation: tperp0, tperp1, tperp2

• "kz0": Constant along a field line, that is initialise only with $k_\Vert = 0$.

• "nl": Two $k_\perp$ modes set to constant amplitude. Controlled by:

  • Overall amplitude: phiinit
  • ky indices of modes: ikk
  • kx indices of modes: itt
  • Parity: even about $\theta_0$ unless chop_side is true, in which case none

• "nl2": Two $k_\perp$ modes proportional to $1 + v_\Vert \sin(\theta)$. Controlled by:

  • Overall amplitude: phiinit
  • ky indices of modes: ikk
  • kx indices of modes: itt
  • Parity: even about $\theta_0$ unless chop_side is true, in which case none

• "nl3": Two $k_\perp$ modes with a Gaussian envelope, and perturbation in fields of form $x_0 + x_1 \cos(\theta) + x_2 \cos(2 \theta)$, except for parallel velocity which uses is 90 degrees out of phase and uses $\sin$. Density, parallel velocity, and perpendicular and parallel temperatures can all be controlled independently. Controlled by:

  • Overall amplitude: phiinit
  • Amplitude of real and imaginary parts of $\phi$: refac, imfac
  • Gaussian envelope width in $\theta$: width0
  • ky indices of modes: ikk
  • kx indices of modes: itt
  • Parity: even about $\theta_0$ unless chop_side is true, in which case none
  • Density perturbation: den0, den1, den2
  • Parallel velocity perturbation: upar0, upar1, upar2
  • Parallel temperature perturbation: tpar0, tpar1, tpar2
  • Perpendicular temperature perturbation: tperp0, tperp1, tperp2

• "nl3r": Similar to "nl3", but includes apar.

• "nl4": Unsupported and inconsistent over time; do not use.
• "nl5": Unsupported; do not use.
• "nl6": Unsupported; do not use.
• "nl7": Unsupported; do not use.
• "ot": Orszag-Tang 2D vortex problem (see aparamp, phiamp, ittt, ikkk)
• "rh": Maxwellian perturbation in ik == 1 mode; do not use?
• "stationary_mode": Initialises the distribution function such that it is a time-independent solution to the gyrokinetic equation when collisions are neglected and only one mode (with aky = 0) is present. See Section 4 of the Analytic Geometry Specification documentation for more details.
• "recon": Unsupported; do not use.
• "recon3": Unsupported; do not use.
• "test3": Unsupported; do not use.
• "xi": Perturbation proportional to pitch angle, $\xi$. Unlikely to be useful.
• "xi2": Perturbation proportional to $1 - 3\xi^2$. Unlikely to be useful.
• "zero": Sets distribution function to zero

Restarting options

These options are used for restarting GS2. See Restarting a simulation for more details.

• "restart", "many", or "file": Restart, using g from restart files. See ginit_restart_many.
• "eig_restart": Uses the restart files written by the eigensolver. File to read is set by restart_eig_id. See ginit_restart_eig

If GS2 has been built with parallel netCDF, then read_many controls whether a single restart file or one file per processor is used.

You can scale the fields from the restart files with scale. Note that if scale is negative, the fields are scaled by -scale / max(abs(phi))!

Less-usual restarting options

These options are also used for restarting, but have additional behaviours. They are not well documented or maintained, so use at your own risk.

• "no_zonal": Restart but remove the zonal flow $(k_y = 0)$ component.
• "small": Add restarted fields to a background as set by the "noise" option.
• "smallflat": Similar to "small", but with a different random background.

• "zonal_only": Restart but set all non-zonal components $(k_y \ne 0)$ of the potential and the distribution function to 0. Input parameters:

  • Noise can be added to these other components by setting phiinit > 0.
  • The size of the zonal flows can be adjusted using zf_init.