parameters

• beta: In general, \(\beta\) is the ratio of kinetic to magnetic energy. In GS2, the parameter \(\beta\) affects only the dynamics, not the equilibrium.
  • For electromagnetic runs, the contribution of each species to the total parallel current is weighted by a factor of \(w_s = 2 \beta Z_s n_s \sqrt{T_s/m_s}\).
  • For electromagnetic runs that include \(\delta B_\parallel\), this field is proportional to \(\beta\).
  • The contribution of \((\delta B)^2\) to the total gyrokinetic energy is inversely proportional to this input parameter.
  • If an antenna is set up to drive Alfven waves, then \(\beta\) is used to calculate the Alfven frequency.
  • For some collision operator models, \(\beta\) is used to calculate the resistivity.
  • For some rarely-used initial conditions, \(\beta\) appears explicitly.
  • Important: \(\beta\) is not automatically set to be consistent with the value of \(\beta\) used to calculate properties of a given magnetic equilibrium. The user is responsible for choosing the gradients, densities, and temperatures of all species to be consistent with the values of \(\beta\) and \(\beta'\) which appear here and elsewhere.
• parameters_k0:
• teti: Ratio of electron to ion temperatures. Deprecated. Do not use unless you know what you are doing.
• tite: Ratio of ion to electron temperatures. This parameter is used only when there is no species called "electron" included.
• zeff: Effective ionic charge. The parameter \(Z_{\mathrm eff}\) appears only in the electron collision frequency, and is not automatically set to be consistent with the mix of species specified in the species namelists.

kt_grids_knobs

• grid_option: The general layout of the grid.
• norm_option: The definition of \(v_{th}\)

Note:Intheinputfile,onlyoneofthefollowingsectionsneedtobeincluded,dependingonthevalueof``\ ```grid_option <grid_option>`__.

kt_grids_box_parameters

• jtwist:
• ly:
• naky: The actual number of ky modes (do not use for nonlinear runs, use ny)
• nkpolar:
• ntheta0:
• nx: The number of kx modes: the number of kx modes actually simulated (ntheta0) is equal to 2*(nx - 1)/3 + 1, due to the need to prevent aliasing.
• ny: The number of ky modes: the number of ky modes actually simulated (naky) is equal to (ny - 1)/3 + 1, due to the need to prevent aliasing.
• rtwist:
• x0: The length of the box in the x direction (measured in the Larmour radius of species 1) if shat is 0 (ie 1e-6)
• y0: The length of the box in the y direction (measured in the Larmour radius of species 1)

kt_grids_single_parameters

• akx:
• aky: \(k_y \rho\) for the reference species. Used only in certain modes (e.g. in single mode).
• theta0:

theta_grid_parameters

• akappa: Sets local elongation when local toroidal equilibrium is specified.
• akappri: Sets local gradient of elongation when local toroidal equilibrium is specified.
• alpmhd: Default = 0. Do not use unless you know what you are doing.
• asym: *asympri:
• asympri:
• eps: Controls particle trapping (among other things) in simple geometric models. \(\epsilon = r/R\)
• epsl: Sets curvature drift in simple geometric models. \(\epsilon_\ell = 2 a / R\), where a is the GS2 normalisation length and R is the major radius at the centre of the flux surface.
• kp: If kp > 0 then pk = 2*kp. Set kp rather than pk in the slab. Since in the slab limit, shat = 2a/ (L_S pk), this means that if kp = 1, shat = a/ L_S, where L_S is the magnetic shear scale length.

Sets parallel box length when geometry is unsheared slab. \(k_p = 2 \pi /L_z\).

• nperiod: Sets the number of \(2\pi\) segments along equilibrium magnetic field to include in simulation domain. \(N_{\mathrm segments} = (2n_{\mathrm period} - 1)\).
• ntheta: Number of grid points along equilibrium magnetic field between \(\theta=(-\pi,\pi)\) (in addition to a grid point at \(\theta=0\)).
• pk: \(p_k = 2 a / q R\) - when using high aspect ratio, \(s-\alpha\) model for geometry it sets q, the magnetic safety factor, since the ratio 2a/R is set by epsl. It therefore also sets the connection length, i.e. the length of the box in the parallel direction, in terms of a, the GS2 normalization quantity.
• qinp: Sets value of the safety factor when using local toroidal equilibrium model.
• r_geo: Major radius
• rhoc: Minor radius
• rmaj: Major radius
• shat: Sets value of magnetic shear in simple geometric models.
• shift: Related to Shafranov shift. Sign depends on geometric model.
• tri: Sets local triangularity when local toroidal equilibrium is specified.
• tripri: Sets local gradient of triangularity when local toroidal equilibrium is specified.

theta_grid_knobs

• equilibrium_option: 's-alpha': Use high aspect-ratio toroidal equilbrium (which can be simplified to slab or cylinder), controlled by the subsidiary namelists theta_grid_parameters and theta_grid_salpha_knobs.
• gb_to_cv:

theta_grid_salpha_knobs

• alpha1:
• alpmhdfac:
• model_option:

theta_grid_file_knobs

• gridout_file:
• no_geo_info:

theta_grid_gridgen_knobs

• alknob:
• bpknob:
• deltaw:
• epsknob:
• extrknob:
• npadd:
• tension:
• thetamax:
• widthw:

theta_grid_eik_knobs

• ak0:
• alpha_input:
• beta_prime_input:
• bishop:
• delrho:
• dfit_eq:
• dp_mult:
• efit_eq:
• eqfile:
• equal_arc:
• gen_eq:
• gs2d_eq:
• idfit_eq:
• iflux:
• invlp_input:
• irho:
• ismooth:
• isym:
• itor:
• k1:
• k2:
• local_eq:
• ppl_eq:
• rmax:
• rmin:
• s_hat_input:
• transp_eq:
• vmom_eq:
• writelots:

le_grids_knobs

• advanced_egrid:
• bouncefuzz:
• ecut:
• le_grids_test:
• negrid: Total number of energy grid points
• nesub:
• nesuper:
• new_trap_int:
• ngauss: # of untrapped pitch-angles moving in one direction along
• nmax:
• nterp:
• testfac:
• trapped_particles:
• vcut: No. of standard deviations from the standard Maxwellian beyond which the distribution function will be set to 0
• vgrid:
• wgt_fac:

dist_fn_knobs

• adiabatic_option:
• afilter:
• apfac:
• boundary_option: Sets the boundary condition along the field line (i.e. the boundary conditions at theta = +- pi). Possible values are:

'zero', 'default', 'unconnected' - Use Kotschenreuther boundary condition at endpoints of theta grid 'self-periodic', 'periodic', 'kperiod=1' - Each mode is periodic in theta with itself 'linked' - Twist and shift boundary conditions 'alternate-zero' - Ignored

• btor_slab:
• d_kill:
• def_parity:
• dist_fn_even:
• driftknob:
• g_exb:
• g_pvg:
• gridfac: Affects boundary condition at end of theta grid.
• h_kill:
• kfilter:
• kill_grid:
• mach:
• mult_imp:
• neoflux:
• noise:
• nperiod_guard:
• omprimfac:
• poisfac:
• save_n:
• test: For debugging
• tpdriftknob:
• wfb:

fields_knobs

• field_option: Advance linear terms with Kotschenreuther's

knobs

• avail_cpu_time: Specify the available wall clock time in seconds. GS2 will exit before this time. This ensures that all the output files are written correctly. CodeRunner automatically sets this quantity unless it is given the value false.
• delt: Timestep, in units of \(a/v_{t0}\). For linear runs, this value does not change. For nonlinear runs, the timestep used by the code will not be allowed to exceed this value.
• delt_option: *margin: Deprecated. Do not use.
• eqzip: Default = .false. Do not evolve certain \(k\) modes in time. Set this to true only if you know what you are doing.
• eqzip_option:
• fapar: Multiplies \(A_\parallel\) throughout. Set to zero for electrostatic calculations, or unity for electromagnetic. Set to zero if \(\beta = 0\).
• faperp: Multiplies A_perp. Use 1 for high beta, 0 otherwise. Deprecated: use fbpar instead. Defaults to zero. Do not change this value unless you know what you are doing.
• fbpar: Multiplies \(B_\parallel\) throughout. Set to zero or unity, depending on whether you want to include physics related to \(\delta B_\parallel\). Set to zero if \(\beta = 0\).
• fphi: Multiplies \(\Phi\) (electrostatic potential) throughout. Useful for debugging.
• harris: Default = .false. Do not set to true unless you know what you are doing.
• margin:
• nstep: Number of timesteps that will be taken, unless the code stops for some (usually user-specified) reason.
• secondary: Default = .false. Do not set to true unless you know what you are doing.
• tertiary: Default = .false. Do not set to true unless you know what you are doing.
• wstar_units: Default = .false. Make the timestep proportional to \(k_y \rho\). This can be useful for linear stability calculations that have a wide range of \(k_y\) values. Do not set to true for nonlinear runs. Be aware that the units of some output quantities can change when wstar_units = .true.

reinit_knobs

• delt_adj: When the time step needs to be changed, it is adjusted
• delt_cushion:
• delt_minimum: The minimum time step is delt_minimum.

layouts_knobs

• layout: 'yxles', 'lxyes', 'lyxes', 'lexys' Strongly affects performance on parallel computers
• local_field_solve: Strongly affects initialization time on some

collisions_knobs

• adjust:
• cfac: Factor multiplying FLR terms in collision operator. 1.0 by default. Set to 0.0 to turn off FLR corrections.
• collision_model: .<<<<<<<<<<<<current

Collision model used in the simulation.

• • default = pitch angle scattering and energy diffusion
  • none = collisionless
  • lorentz = pitch angle scattering only
  • ediffuse = energy diffusion only

.>>>>>>>>>>>>new

Collision model used in the simulation.

• conservative: Set to .true. to guarantee exact conservation properties.
• conserve_moments: Set to .true. to guarantee collision operator conserves momentum and energy.
• const_v:
• ediff_scheme:
• ei_coll_only:
• heating: Set to .true. to compute collisional heating.
• hypermult:
• lorentz_scheme:
• resistivity:
• test_collisions:

hyper_knobs

• const_amp:
• d_hyper:
• d_hyperres:
• d_hypervisc:
• gridnorm:
• hyper_option: 'default' is 'none'
• include_kpar:
• isotropic_shear:
• nexp:
• omega_osc:

nonlinear_terms_knobs

• c_par:
• c_perp:
• cfl: The maximum delt < cfl * min(Delta_perp/v_perp)
• flow_mode:
• nonlinear_mode: 'on' Include nonlinear terms.
• p_x:
• p_y:
• p_z:
• zip:

additional_linear_terms_knobs

species_knobs

• nspec: Number of kinetic species evolved.

species_parameters

• dens: Density
• dens0:
• fprim: 2.22 !-1/n (dn/drho)
• mass: Mass
• nu:
• nu_h:
• nustar:
• temp: Temperature
• tpar0:
• tperp0:
• tprim: 6.0 !-1/T (dT/drho)
• type: 'ion' Thermal ion species
• u0:
• uprim: ?
• uprim2:
• vnewk: 1.e-2 !collisionality parameter
• z: Charge

dist_fn_species_knobs

• bakdif: 0.0 !Spatial implicitness parameter. Recommended value: 0.05
• bd_exp:
• fexpi:
• fexpr: 0.5 !Temporal implicitness parameter. Recommended value: 0.48

init_g_knobs

• a0:
• adj_spec:
• apar0:
• b0:
• chop_side: Rarely needed. Forces asymmetry into initial condition.
• den0: Parameters for setting up special initial conditions.
• den1: Parameters for setting up special initial conditions.
• den2:
• dphiinit:
• eq_mode_n:
• eq_mode_u:
• eq_type:
• even:
• ginit_option: ???
• ikk:
• ikkk:
• ikpar_init:
• imfac: Used in rare cases.
• input_check_recon:
• itt:
• ittt:
• k0: Available for highly specialized initial conditions. Do not use unless you know what you are doing.
• kpar_init:
• left:
• new_field_init:
• nkxy_pt:
• null_apar:
• null_bpar:
• null_phi:
• phifrac:
• phiinit: Average amplitude of initial perturbation of each
• phiinit0:
• prof_width:
• refac: Used in rare cases.
• restart_dir:
• restart_file: Base of filenames with restart data.
• scale:
• tpar0:
• tpar1:
• tpar2:
• tperp0:
• tperp1:
• tperp2:
• tstart:
• ukxy_pt:
• upar0: Parameters for setting up special initial conditions.
• upar1: Parameters for setting up special initial conditions.
• upar2:
• width0: Initial perturbation has Gaussian envelope in theta with width width0,
• zf_init:

gs2_diagnostics_knobs

• dump_check1:
• dump_check2:
• dump_fields_periodically:
• dump_final_xfields:
• dump_neoclassical_flux:
• exit_when_converged:
• igomega:
• make_movie:
• navg: Any time averages performed over navg
• nmovie:
• nperiod_output:
• nsave: Write restart files every nsave timesteps
• nwrite: Output diagnostic data every nwrite
• omegatinst: Recommended value: 500.
• omegatol: In linear runs GS2 will exit if the growth rate has converged to an accuracy of omegatol. Set negative to switch off this feature.
• print_flux_line: Instantaneous fluxes output to screen
• print_line: Estimated frequencies and growth rates to the stdout
• print_old_units: If false print internal code units. Deprecated
• save_for_restart: If true then restart files written to the local folder and the simulation can be restarted from the point it ended.
• test_conserve: Plots zonal flow component (ie. ky=0,kz=0) of moments of h vs time into NetCDF file
• use_shmem_for_xfields:
• write_apar: Deprecated
• write_aperp: Deprecated
• write_ascii:
• write_avg_moments: Ignored unless grid_option='box'. Write n, T as a fn of time (as a fn of kx, ky?)
• write_bpar:
• write_cerr:
• write_cross_phase:
• write_dmix: If (write_ascii = T) write D_ML to output file.
• write_eavg: Time averaged turbulent fluxes as a function of energy (E)
• write_eigenfunc: If (write_ascii = T) Normalized Phi
• write_epartot:
• write_epolar:
• write_fcheck:
• write_fieldcheck:
• write_fieldline_avg_phi: * write_final_epar: If (write_ascii = T) E_parallel(theta)
• write_fields:
• write_final_antot:
• write_final_epar: If (write_ascii = T) E_parallel(theta)
• write_final_fields: If (write_ascii = T) Phi(theta) written to '.fields'
• write_final_moments: write final n, T
• write_flux_line:
• write_full_moments_notgc:
• write_g: Write the distribution function to the '.dist' (NetCDF?)
• write_gg:
• write_gs:
• write_gyx: Write dist fn at a given physical spacial point to a file
• write_hrate: Write heating rate, collisonal entropy generation etc to '.heat'
• write_kpar:
• write_kperpnorm:
• write_lamavg: Time averaged turbulent fluxes as a function of lambda (= mu/E)
• write_line: If (write_ascii = T) estimated frequencies and growth rates to the output file
• write_lorentzian: Frequency Sweep Data
• write_lpoly:
• write_max_verr:
• write_neoclassical_flux:
• write_nl_flux: Phi**2(kx,ky) written to runname.out
• write_omavg: If (write_ascii = T) time-averaged growth rate and frequency to the output file.
• write_omega: If (write_ascii = T) instantaneous omega to output file? very heavy output
• write_parity: Writes parities in dist fn and particle fluxes
• write_pbflux:
• write_pflux:
• write_phi: No longer used.
• write_phitot:
• write_pmflux:
• write_qbheat:
• write_qheat: * write_stress: Klaus Hallacek's diagnostic for toroidal stress... see his (unpublished) paper
• write_qmheat:
• write_stress: Klaus Hallacek's diagnostic for toroidal stress... see his (unpublished) paper
• write_tavg: Time averaged turbulent fluxes as a function of theta
• write_vbflux:
• write_verr: Write velocity space diagnostics to '.lpc' and '.verr' files
• write_vflux:
• write_vmflux:
• write_vortcheck:

testgridgen

• alknob:
• auto_width:
• bpknob:
• cv_fraction:
• deltaw:
• delth_max:
• epsknob:
• extrknob:
• gingrid:
• gsource:
• iperiod:
• max_autoiter:
• nfinegrid:
• nlambdaout:
• npadd:
• nperiodout:
• nthetaout:
• screenout:
• smoothknob:
• source:
• tension:
• thetamax:
• three_dim:
• widthw:

driver

• amplitude:
• ant_off:
• driver_t0:
• nk_stir:
• restarting:
• w_antenna:
• w_dot:
• write_antenna:

stir

• stir_a:
• stir_b:
• stir_kx:
• stir_ky:
• stir_kz:
• stir_travel:

source_knobs

• a_ext:
• akx_star:
• aky_star:
• gamma0:
• omega0:
• phi_ext:
• source0:
• source_option:
• t0:
• thetas:

kt_grids_range_parameters

• aky_max:
• aky_min:
• naky: the number of 'actual' ky modes.
• ntheta0:
• theta0_max:
• theta0_min:

kt_grids_specified_parameters

• naky:
• ntheta0:
• nx:
• ny:

kt_grids_specified_element

• akx:
• aky:
• theta0:

kt_grids_xbox_parameters

• aky:
• lx:
• ntheta0:
• nx:

gs2_flux_knobs

• delta:
• flux_eps:
• flux_option:
• nflux:

flux_target

• heat: