# Alphabetical list for input.cgyro¶

## AMP¶

**Definition**

Initial amplitude of finite-\(n\) modes.

**Comments**

DEFAULT = 0.1

For linear simulations, the value is unimportant

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

## BETAE_UNIT¶

**Comments**

DEFAULT = 0.0

**Definition**

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

**Comments**

DEFAULT = 0.0

## BETA_STAR_SCALE¶

**Definition**

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

**Comments**

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.

**Comments**

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, \(L_0 = r/(qs)\).

**Comments**

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)

**Comments**

DEFAULT = 4

To control conservation and other properties, the following parameters can be set: COLLISION_FIELD_MODEL, COLLISION_MOM_RESTORE, COLLISION_ENE_RESTORE, COLLISION_ENE_DIFFUSION, COLLISION_KPERP

On GPU systems, GPU offload is controlled by GPU_BIGMEM_FLAG. When that is not enabled, the slower but less GPU memory demanding CPU-only Sugama operator is used.

## 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

**Comments**

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

**Comments**

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

**Comments**

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

**Comments**

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

**Comments**

DEFAULT = 1

For test purposes only.

## DELTA¶

**Definition**

Triangularity, \(\delta\), of the flux surface:

**Comments**

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 \((c_s/a) \Delta t\).

**Comments**

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)

**Comments**

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.

**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:

**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:

**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 (\(\theta=0\)).

## E_MAX¶

**Definition**

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

**Comments**

DEFAULT = 8.0

Corresponds to Maxwellian factor \(\displaystyle e^{-\varepsilon_\mathrm{max}}\)

## ERROR_TOL¶

**Definition**

Error tolerance for adaptive time-stepping.

**Comments**

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

**Comments**

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 \(\delta B_\parallel(k_x^0,k_y,t)\) .

**Comments**

DEFAULT = 0

Output files are

`bin.cgyro.kxky_apar`

and`bin.cgyro.kxky_bpar`

, respectivelyEven 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.

**Comments**

DEFAULT = 0.001

## GAMMA_E¶

**Definition**

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

**Comments**

DEFAULT = 0.0

See discussion on plasma rotation

## GAMMA_E_SCALE¶

**Definition**

Scaling factor applied to experimental value of \(\gamma_E\) .

**Comments**

DEFAULT = 1.0

Only active for PROFILE_MODEL =2

## GAMMA_P¶

**Definition**

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

**Comments**

DEFAULT = 0.0

See discussion on plasma rotation

## GAMMA_P_SCALE¶

**Definition**

Scaling factor applied to experimental value of \(\gamma_p\) .

**Comments**

DEFAULT = 1.0

Only active for PROFILE_MODEL =2

## GPU_BIGMEM_FLAG¶

**Definition**

Enable (or disable) memory intensive GPU offload.

**Comments**

DEFAULT = 0

Only active on GPU systems for COLLISION_MODEL =4

## H_PRINT_FLAG¶

**Definition**

Toggle printing of distribution for single-mode runs.

**Comments**

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.

**Comments**

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.

**Comments**

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.

**Comments**

DEFAULT = 0

See also N_GLOBAL

## KY¶

**Definition**

Selector for value of \(k_\theta \rho_s\) .

**Comments**

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

## MACH¶

**Definition**

Rotation speed (Mach number) \(M\)

**Comments**

DEFAULT = 0.0

See discussion in plasma rotation

## MACH_SCALE¶

**Definition**

Scaling factor applied to experimental value of \(M\) .

**Comments**

DEFAULT = 1.0

Only active for PROFILE_MODEL =2

## MASS_*¶

**Definition**

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

**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

## MOMENT_PRINT_FLAG¶

**Definition**

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

**Comments**

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

**Comments**

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

**Comments**

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 \((\delta\phi,\delta A_\parallel,\delta B_\parallel)\)

**Comments**

DEFAULT = 1

## N_GLOBAL¶

**Definition**

Control number of global output harmonics

**Comments**

DEFAULT = 4

Making this larger retains shorter scales in the output

## NU_GLOBAL¶

**Definition**

Source rate

**Comments**

DEFAULT = 15.0

Making this larger increases the source rate

## NU_EE¶

**Definition**

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

**Comments**

DEFAULT = 0.1

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

The recommended

*minimum value*is NU_EE = 0.01.

## N_RADIAL¶

**Definition**

Number of radial wavenumbers to retain in simulation.

**Comments**

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.

**Comments**

DEFAULT = 24

## N_XI¶

**Definition**

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

**Comments**

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

**Comments**

DEFAULT = 8

This is the

**energy resolution**This is equivalent to number of retained Laguerre polynomials

## Q¶

**Definition**

Safety factor, \(q\), of the flux surface.

**Comments**

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.

## RESTART_STEP¶

## RMIN¶

**Definition**

The ratio \(r/a\), where \(r\) is the minor radius and \(a\) is the radius of the LCFS.

**Comments**

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.

**Comments**

DEFAULT = 3.0

## ROTATION_MODEL¶

**Definition**

**Choices**

ROTATION_MODEL = 1: Weak rotation

ROTATION_MODEL = 2: Sonic (Sugama) rotation

**Comments**

DEFAULT = 1

## S¶

**Definition**

Magnetic shear, \(s\), of the flux surface:

**Comments**

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:

**Comments**

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.

## S_DELTA¶

**Definition**

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

**Comments**

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:

**Comments**

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.

## TEMP_*¶

**Definition**

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

**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 \(T_e\).

## Z_*¶

**Definition**

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

**Comments**

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.

**Comments**

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.