# Alphabetical list for input.cgyro¶

## AMP¶

Definition

Initial amplitude of finite-$$n$$ modes.

• DEFAULT = 0.1

• For linear simulations, the value is unimportant

• For nonlinear runs, this will usually need to be reduced to a smaller value.

## AMP0¶

Definition

Initial amplitude of $$n = 0$$ modes.

• DEFAULT = 0.0

## BETAE_UNIT¶

• DEFAULT = 0.0

Definition

The electron beta with reference to $$B_\mathrm{unit}$$:

$\beta_{e,\mathrm{unit}} \doteq \frac{8 \pi n_e T_e}{B_\mathrm{unit}^2}$

• DEFAULT = 0.0

## BETAE_UNIT_SCALE¶

Definition

Scale factor for BETAE_UNIT.

• DEFAULT = 1.0

## BETA_STAR_SCALE¶

Definition

Pressure gradient scaling factor. Here, the pressure gradient factor is defined as

$\beta_* = - \frac{8\pi}{B_\mathrm{unit}^2} \frac{dp}{dr}$

• DEFAULT = 1.0

• In the absence of scaling, the value of $$\beta_*$$ will be computed self-consistently given the value of $$\beta_{e,\mathrm{unit}}$$ set in BETAE_UNIT.

• Often it is desired to reduce $$\beta_{e,\mathrm{unit}}$$ but leave the effective $$\beta_*$$ unchanged. In this case, one should divide BETAE_UNIT by 2, then set BETA_STAR_SCALE=2.

## BTCCW¶

Definition

Parameter which selects the orientation of the toroidal magnetic field $$B_t$$ relative to the toroidal angle $$\varphi$$.

Choices

• BTCCW = 1: Counter-clockwise when viewed from above the torus - negative $$\mathbf{e}_{\varphi}$$ for the right-handed coordinate system $$(r,\theta,\varphi)$$. Thus, $$B_t$$ is oriented along the negative $$\mathbf{e}_{\varphi}$$ direction.

• BTCCW = -1: Clockwise when viewed from above the torus - positive $$\mathbf{e}_{\varphi}$$ for the right-handed coordinate system $$(r,\theta,\varphi)$$. Thus, $$B_t$$ is oriented along the positive $$\mathbf{e}_{\varphi}$$ direction.

• DEFAULT = -1

• In DIII-D, typically BTCCW = 1.

• When experimental profiles are used (PROFILE_MODEL = 2), the orientiation of $$B_t$$ is inferred from input.profiles.

## BOX_SIZE¶

Definition

Factor to determine the radial box length, $$L_x$$, as a multiple of the distance between reference singular surfaces, $$L_0 = r/(qs)$$.

$\frac{L_x}{a} = \mathrm{BOX\_SIZE} \; \left( \frac{r}{qs} \right)$

• DEFAULT = 1.0

• Note that the reference singular surface spacing refers to $$n=1$$ which is always the lowest non-zero mode in CGYRO.

• Also, $$r \rightarrow$$ RMIN, $$s \rightarrow$$ S, $$q \rightarrow$$ Q.

## COLLISION_MODEL¶

Definition

Collision operator selection.

Choices

• COLLISION_MODEL = 1: Lorentz ee+ei

• COLLISION_MODEL = 2: Connor

• COLLISION_MODEL = 4: Sugama (maximal accuracy)

• COLLISION_MODEL = 5: Simple Lorentz ee+ei (fastest)

## COLLISION_FIELD_MODEL¶

Definition

Flag to toggle self-consistent field update during collisions.

Choices

• COLLISION_FIELD_MODEL = 0: Field update OFF

• COLLISION_FIELD_MODEL = 1: Field update ON

• DEFAULT = 1

## COLLISION_MOM_RESTORE¶

Definition

Flag to toggle collisional momentum conservation.

Choices

• COLLISION_MOM_RESTORE = 0: Momentum conservation OFF

• COLLISION_MOM_RESTORE = 1: Momentum conservation ON

• DEFAULT = 1

• For test purposes only.

## COLLISION_ENE_RESTORE¶

Definition

Flag to toggle collisional energy conservation.

Choices

• COLLISION_ENE_RESTORE = 0: Energy conservation OFF

• COLLISION_ENE_RESTORE = 1: Energy conservation ON

• DEFAULT = 1

• For test purposes only.

## COLLISION_ENE_DIFFUSION¶

Definition

Flag to toggle collisional energy diffusion.

Choices

• COLLISION_ENE_DIFFUSION = 0: Energy diffusion OFF

• COLLISION_ENE_DIFFUSION = 1: Energy diffusion ON

• DEFAULT = 1

• For test purposes only.

## COLLISION_KPERP¶

Definition

Flag to toggle $$k_\perp^2$$ terms in collision operator.

Choices

• COLLISION_KPERP = 0: Terms OFF

• COLLISION_KPERP = 1: Terms ON

• DEFAULT = 1

• For test purposes only.

## DELTA¶

Definition

Triangularity, $$\delta$$, of the flux surface:

• DEFAULT = 0.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the triangularity as a function of radius is read from input.profiles.

## DELTA_T¶

Definition

Simulation timestep $$(c_s/a) \Delta t$$.

• DEFAULT = 0.01

• Because CGYRO uses an explicit time-integration scheme for collisionless terms, the timestep must typically be smaller than for long-wavelength GYRO simulations.

## DELTA_T_METHOD¶

Definition

Control for adaptive or fixed time-stepping.

Choices

• DELTA_T_METHOD = 0: RK4 4:4(3) [non-adaptive]

• DELTA_T_METHOD = 1: Cash-Karp 6:5(4)

• DELTA_T_METHOD = 2: Bogacki-Shampine 7:5(4)

• DELTA_T_METHOD = 3: Verner 10:7(6)

• DEFAULT = 0

• Notation is s:o(e) where s=stages,o=order,e=order of error estimate.

## DENS_*¶

Definition

The normalized equilibrium-scale density. First species density is DENS_1, and so on.

$\mathrm{DENS}* = \frac{n_{*}}{n_e}$

Commments

• DEFAULT = $$[1,0,0,\ldots]$$

• The user should set DENS=1 for electrons.

• When experimental profiles are used (PROFILE_MODEL = 2), the densities are automatically normalized to $$n_e$$.

• When rotation effects are included (ROTATION_MODEL = 2), this parameter is the density at the outboard midplane ($$\theta=0$$).

## DLNNDR_*¶

Definition

The normalized equilibrium-scale density gradient scale length:

$\mathrm{DLNNDR}\_* = -a \frac{\partial {\rm ln} n_{*}}{\partial r}$

Commments

• DEFAULT = $$[1,1,1,\ldots]$$

• When experimental profiles are used (PROFILE_MODEL = 2), the density as a function of radius is read from input.profiles and the gradient is computed internally. The normalizing length is the plasma minor radius.

• When rotation effects are included (ROTATION_MODEL = 2), this parameter is the value at the outboard midplane ($$\theta=0$$).

## DLNTDR_*¶

Definition

The normalized equilibrium-scale temperature gradient scale length:

$\mathrm{DLNTDR}\_* = -a \frac{\partial {\rm ln} T_{*}}{\partial r} \; .$

Commments

• DEFAULT = $$[1,1,1,\ldots]$$

• When experimental profiles are used (PROFILE_MODEL = 2), the temperature as a function of radius is read from input.profiles and the gradient is computed internally. The normalizing length is the plasma minor radius.

• When rotation effects are included (ROTATION_MODEL = 2), this parameter is the value at the outboard midplane ($$\theta=0$$).

## DZMAG¶

Definition

Rate of change of plasma elevation:

$a \frac{\partial Z_0(r)}{\partial r} \; .$

## E_MAX¶

Definition

Maximum value of (pseudospectral) dimensionless energy, $$\varepsilon_\mathrm{max}$$

• DEFAULT = 8.0

• Corresponds to Maxwellian factor $$\displaystyle e^{-\varepsilon_\mathrm{max}}$$

## ERROR_TOL¶

Definition

Error tolerance for adaptive time-stepping.

• DEFAULT = 1e-4

• Decrease this slightly for very-high-transport cases

## EQUILIBRIUM_MODEL¶

Definition

Flux-surface shape specification parameter.

Choices

• EQUILIBRIUM_MODEL = 1: $$s$$ - $$\alpha$$

• EQUILIBRIUM_MODEL = 2: Miller parameterization

• EQUILIBRIUM_MODEL = 3: General (Fourier) parameterization

• DEFAULT = 2

• EQUILIBRIUM_MODEL=1 is not available for experimental profiles (PROFILE_MODEL =2).

## FIELD_PRINT_FLAG¶

Definition

Toggle printing of $$\delta A_\parallel(k_x^0,k_y,t)$$ and $$\delta B_\parallel(k_x^0,k_y,t)$$ .

• DEFAULT = 0

• Output files are bin.cgyro.kxky_apar and bin.cgyro.kxky_bpar, respectively

• Even if this flag is set to zero, potential fluctuations $$\delta\phi(k_x^0,k_y,t)$$ are written to bin.cgyro.kxky_phi

## FREQ_TOL¶

Definition

Eigenvalue convergence tolerance for linear simulations.

• DEFAULT = 0.001

## GAMMA_E¶

Definition

Normalized $$\mathbf{E}\times\mathbf{B}$$ shearing rate $$\displaystyle \frac{a}{c_s} \gamma_E$$.

## GAMMA_E_SCALE¶

Definition

Scaling factor applied to experimental value of $$\gamma_E$$ .

## GAMMA_P¶

Definition

Normalized rotation shearing rate $$\displaystyle \frac{a}{c_s} \gamma_p$$.

## GAMMA_P_SCALE¶

Definition

Scaling factor applied to experimental value of $$\gamma_p$$ .

## GPU_BIGMEM_FLAG¶

Definition

Enable (or disable) memory intensive GPU offload.

## H_PRINT_FLAG¶

Definition

Toggle printing of distribution for single-mode runs.

• DEFAULT = 0.

## IPCCW¶

Definition

Parameter which selects the orientation of the plasma current (and thus the poloidal magnetic field $$B_p$$) relative to the toroidal angle $$\varphi$$.

Choices

• IPCCW = 1: Counter-clockwise when viewed from above the torus - negative $$\mathbf{e}_{\varphi}$$ for the right-handed coordinate system $$(r,\theta,\varphi)$$. Thus, $$B_p$$ is oriented along the negative $$\mathbf{e}_{\varphi}$$ direction.

• IPCCW = -1: Clockwise when viewed from above the torus - positive $$\mathbf{e}_{\varphi}$$ for the right-handed coordinate system $$(r,\theta,\varphi)$$. Thus, $$B_p$$ is oriented along the positive $$\mathbf{e}_{\varphi}$$ direction.

• DEFAULT = -1

• In DIII-D, typically IPCCW = 1.

• When experimental profiles are used (PROFILE_MODEL = 2), the orientiation of IP is inferred from input.profiles.

## KAPPA¶

Definition

Elongation, $$\kappa$$, of the flux surface.

• DEFAULT = 1.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the elongation as a function of radius is read from input.profiles.

## GFLUX_PRINT_FLAG¶

Definition

Toggle printing of global flux profiles.

## KY¶

Definition

Selector for value of $$k_\theta \rho_s$$ .

• If N_TOROIDAL = 1, this is the simulated value of $$k_\theta \rho_s$$

• If N_TOROIDAL > 1, this is the lowest nonzero value of $$k_\theta \rho_s$$

• Use the output in out.cgyro.info to guide selection of KY

Definition

Definition

## MACH¶

Definition

Rotation speed (Mach number) $$M$$

## MACH_SCALE¶

Definition

Scaling factor applied to experimental value of $$M$$ .

## MASS_*¶

Definition

The species mass normalized to deuterium mass: MASS_1, and so on.

${\rm MASS}\_* = \frac{m_*}{m_D} \; .$

Commments

• DEFAULT = $$[1,1,1,\ldots]$$

• When experimental profiles are used (PROFILE_MODEL = 2), the normalizing mass is deuterium.

• A typical case (deuterium, carbon, electrons) would be:

MASS_1=1.0
MASS_2=6.0
MASS_3=2.724e-4


## MAX_TIME¶

Definition

Maximum simulation time in units of $$a/c_s$$

## MOMENT_PRINT_FLAG¶

Definition

Toggle printing of $$\delta n_a(k_x^0,k_y,t)$$ and $$\delta E_a(k_x^0,k_y,t)$$ .

• DEFAULT = 0.

## MPI_RANK_ORDER¶

Definition

Specify the relative ordering of MPI ranks.

Choices

• MPI_RANK_ORDER = 1: Depth-first mode

• MPI_RANK_ORDER = 2: Breadth-first mode

• DEFAULT = 2

• The optimal value depends on both the hardware and the problem being run.

## NONLINEAR_FLAG¶

Definition

Toggle inclusion of nonlinear terms.

Choices

• NONLINEAR_FLAG=0: Nonlinear terms OFF

• NONLINEAR_FLAG=1: Nonlinear terms ON

• DEFAULT = 0

## N_FIELD¶

Definition

Selector for number of fluctuating fields

Choices

• N_FIELD=1: Retain $$\delta\phi$$

• N_FIELD=2: Retain $$(\delta\phi,\delta A_\parallel)$$

• N_FIELD=3: Retain $$(\delta\phi,\delta A_\parallel,\delta B_\parallel)$$

• DEFAULT = 1

## N_GLOBAL¶

Definition

Control number of global output harmonics

• DEFAULT = 4

• Making this larger retains shorter scales in the output

## NU_GLOBAL¶

Definition

Source rate

• DEFAULT = 15.0

• Making this larger increases the source rate

Definition

Definition

Definition

Definition

Definition

## NU_EE¶

Definition

Electron-electron collision frequency $$\nu_{ee}$$, in units of $$c_s/a$$.

$\nu_{ee} = \frac{4\pi n_e e^4}{(2T_e)^{3/2} m_e^{1/2}} \,\log\Lambda \; .$

• DEFAULT = 0.1

• All ion collision rates are self-consistently determined from NU_EE.

• The recommended minimum value is NU_EE = 0.01.

Definition

Number of radial wavenumbers to retain in simulation.

• DEFAULT = 4

• For linear simulations with BOX_SIZE =1, this can be as small as 2, but a minimium of 4 is recommended.

• Wavenumbers span $$p = -N , \ldots , N-1$$ where $$N$$ = N_RADIAL/2

## N_THETA¶

Definition

Number of poloidal gridpoints $$\theta_i$$ to retain in simulation.

• DEFAULT = 24

## N_XI¶

Definition

Number of Legendre pseudospectral meshpoints $$\xi_i$$ to retain in simulation.

• DEFAULT = 16

• This is the pitch-angle resolution

• This is equivalent to number of retained Legendre polynomials

## N_ENERGY¶

Definition

Number of generalized-Laguerre pseudospectral meshpoints $$v_i$$ to retain in simulation

• DEFAULT = 8

• This is the energy resolution

• This is equivalent to number of retained Laguerre polynomials

Definition

Definition

Definition

## Q¶

Definition

Safety factor, $$q$$, of the flux surface.

• DEFAULT = 2.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the safety factor as a function of radius is read from input.profiles and the safety factor gradient is computed internally.

## RMIN¶

Definition

The ratio $$r/a$$, where $$r$$ is the minor radius and $$a$$ is the radius of the LCFS.

• DEFAULT = 0.5

## RMAJ¶

Definition

The ratio $$R_0/a$$, where $$R_0$$ is the major radius and $$a$$ is the radius of the LCFS.

• DEFAULT = 3.0

## ROTATION_MODEL¶

Definition

Choices

• ROTATION_MODEL = 1: Weak rotation

• ROTATION_MODEL = 2: Sonic (Sugama) rotation

• DEFAULT = 1

## S¶

Definition

Magnetic shear, $$s$$, of the flux surface:

$s = \frac{r}{q} \frac{\partial q}{\partial r} \; .$

• DEFAULT = 1.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the safety factor as a function of radius is read from input.profiles and the safety factor gradient is computed internally.

## SHIFT¶

Definition

Shafranov shift, $$\Delta$$, of the flux surface:

$\Delta = \frac{\partial R_0}{\partial r} \; .$

• DEFAULT = 0.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the flux-surface-center major radius as a function of radius, $$R_0(r)$$, is read from input.profiles and its derivative is computed internally.

## SHAPE_COS0¶

Definition

0th antisymmetric moment.

• DEFAULT = 0.0

## SHAPE_S_COS0¶

Definition

0th antisymmetric moment shear.

• DEFAULT = 0.0

## SHAPE_COS1¶

Definition

1st antisymmetric moment.

• DEFAULT = 0.0

## SHAPE_S_COS1¶

Definition

1th antisymmetric moment shear.

• DEFAULT = 0.0

## SHAPE_COS2¶

Definition

2nd antisymmetric moment.

• DEFAULT = 0.0

## SHAPE_S_COS2¶

Definition

2th antisymmetric moment shear.

• DEFAULT = 0.0

## SHAPE_COS3¶

Definition

3rd antisymmetric moment.

• DEFAULT = 0.0

## SHAPE_S_COS3¶

Definition

3rd antisymmetric moment.

• DEFAULT = 0.0

## SHAPE_SIN3¶

Definition

3rd symmetric moment.

• DEFAULT = 0.0

## SHAPE_S_SIN3¶

Definition

3rd symmetric moment shear.

• DEFAULT = 0.0

Definition

## S_DELTA¶

Definition

Measure of the rate of change of the average triangularity of the flux surface:

$s_\delta = r \, \frac{\partial \delta}{\partial r} \; .$

• DEFAULT: 0.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the triangularity as a function of radius is read from input.profiles and the triangularity gradient is computed internally.

## S_KAPPA¶

Definition

Measure of the rate of change of the elongation of the flux surface:

$s_\kappa = \frac{r}{\kappa} \frac{\partial \kappa}{\partial r} \; .$

• DEFAULT: 0.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the elongation as a function of radius is read from input.profiles and the elongation gradient is computed internally.

Definition

## TEMP_*¶

Definition

The normalized equilibrium-scale temperature. First species temperature is TEMP_1, and so on.

$\mathrm{TEMP}\_* = \frac{T_{*}}{T_e} \; .$

Commments

• DEFAULT: TEMP_*= $$[1,\ldots]$$

• The user should set TEMP=1 for electrons.

• When experimental profiles are used (PROFILE_MODEL = 2), the temperatures are automatically normalized to $$T_e$$.

Definition

Definition

## Z_*¶

Definition

Species charge. First species charge is Z_1, and so on.

• DEFAULT = 1

• A typical case (deuterium, carbon, electrons) would be:

Z_1=1
Z_2=6
Z_3=-1


## ZETA¶

Definition

Squareness, $$\zeta$$, of the flux surface.

• DEFAULT = 0.0

• This is only active with EQUILIBRIUM_MODEL = 2 (the Miller equilibrium model).

• When experimental profiles are used (PROFILE_MODEL = 2), the squareness as a function of radius is read from input.profiles.

Definition

Definition