new_gs2_diagnostics_config_type Derived Type

Does the related namelist exist in the target input file?

Used to hold the specific index of numbered namelists

Do we want to skip the read step in init?

Do we want to skip the broadcast step in init?

Append output data to a previous output file <run name>.out.nc if it already exists. Grid sizes must be unchanged.

Used for Trinity nonlinear convergence check (use_nonlin_convergence). The maximum number of time steps, after which consider the run converged regardless.

Used for the Trinity nonlinear convergence check (use_nonlin_convergence). The minimum number of time steps before convergence condition can trigger an exit.

Used for the Trinity nonlinear convergence check (use_nonlin_convergence). The number of timesteps the convergence condition averages over

Used for the Trinity nonlinear convergence check (use_nonlin_convergence). The number of steps where convergence is true before convergence is accepted

Used for the Trinity nonlinear convergence check (use_nonlin_convergence). Multiplier for the cumulative average of the heat flux

Write out the field-line average of $\phi$ to dump.check1. This option is usually used for Rosenbluth-Hinton calculations.

Write out $A_\parallel(k_x, k_y)$ at igomega to <run name>.dc2.

Write out $\phi, A_\parallel, B_\parallel$ to dump.fields.t=(time) every 10 * nwrite timesteps.

Enable parallel IO in the .out.nc file. Currently disabled by default and doesn't activate feature when set to true as we hard code that parallel IO isn't supported for the .out.nc file.

Exit when the run has reached convergence

Verify that the restart file(s) can be written before starting the run

Index in $\theta$ to measure various diagnostics at. By default, this is the outboard midplane $\theta = 0$, but it may be useful to set this to a non-zero value for tearing parity modes.

Write out $\phi, A_\parallel, B_\parallel$ in real space over time, suitable for creating animations. Timestep period is controlled with nmovie

Number of timesteps to average over for time-averaged diagnostics

correction by varying collisionality. But doesn't happen on timesteps when diagnostics are written.

Sets the number of output steps between syncing the netcdf file. Higher values may reduce disk overheads but increase the risk of data loss on unclean exit.

Timestep period to write real space fields $\phi, A_\parallel, B_\parallel$

Timestep period for writing restart data if save_for_restart is .true.. Negative values disable the periodic checkpoints.

Timestep period for writing outputs

Timestep period multiplier for certain "large" diagnostics, which are written every nwrite_mult * nwrite timesteps.

FIXME: What datasets? phicorr_sum, phiextend_sum in old diagnostics, f and fyx in new diagnostics?

If .true., write moments at the outboard midplane only, as opposed to along the entire flux surface

Threshold complex frequency ($\Omega$) for detecting a numerical instability. If $\abs(\Omega)$ averaged over navg timesteps is greater than omegatinst, abort the run.

Frequency ($\omega$) convergence tolerance. Consider the simulation converged and finish the run if $\omega$ has changed by less than omegatol over the last navg timesteps.

More explicitly, the convergence criterion is:

$$\sqrt{\sum_t^{n_{avg}} |\bar{\omega} - \omega|^2} < \min{\bar{\omega}, 1.0}\cdot\omega_{tol}$$

where $\bar{\omega}$ is $\omega$ averaged over the last navg timesteps.

Print the instantaneous fluxes to screen/stdout every nwrite timesteps

Print estimated frequencies and growth rates to screen/stdout every nwrite timesteps

Write the distribution function to <rootname>.nc.dfn.<processor> files. Only written at end of simulation

Write restart files at the end of the simulation. If nsave is positive, then also enable checkpoints by writing restart files every nsave timesteps.

Save some layout and distribution information in restart files

If .true., write one restart file per processor, otherwise write a single restart file.

If gs2 has not been built with parallel netCDF, save_many is ignored and there is always one file per processor (equivalent to save_many = .true.).

If write_many is enabled, you probably want to also set read_many in order to restart from multiple files.

Save parallel and perpendicular velocities in final restart and/or distribution function files

For nonlinear runs, stop the run when the averaged differential of the summed averaged heat flux drops below a threshold for a period of time, controlled by conv_test_multiplier, conv_nsteps_converged, gs2_diagnostics_knobs, conv_max_step, and conv_min_step.

If .false., skip writing any diagnostics

Write the entire $A_\parallel$ field every nwrite timesteps

Write diagnostics to text files. Generally this creates a different text file for each diagnostic. Note that this independent of whether or not netCDF files are used.

FIXME: Verify old and new diagnostics write these files in same format

Write flux surface averaged low-order moments of $g$ every nwrite timesteps

Write the entire $B_\parallel$ field every nwrite timesteps

Write the collision error every nwrite timesteps to text file with suffix .cres

FIXME: What does this mean?

Write collisional heating (collisional and hyper viscous rate of loss of free energy for each mode) every nwrite timesteps

Write two point parallel correlation function calculated from the electric potential as a function of $k_y$ and parallel separation every nwrite timesteps

Write two point parallel correlation function calculated from the electric potential as a function of $k_y$ and parallel separation, time averaged and calculated along the extended domain every nwrite timesteps once istep > nstep/4.

Write the cross phase between electron density and perpendicular electron temperature every nwrite timesteps. Calculated at both the outboard midplane, averaged across $x$ and $y$; and averaged across all space

Write the whole non-adiabatic part of the density moment every nwrite timesteps

Write $\phi, A_\parallel, B_\parallel$ normalised to the value of $\phi$ at the outboard midplane every nwrite timesteps.

If write_ascii is enabled, the text file is <runname>.eigenfunc.

Enable writing $\phi, A_\parallel, B_\parallel$ every nwrite timesteps

Write the right-hand sides of the field equations at the final timestep. If write_ascii is enabled, the file suffix is .antot

Write $\delta B$ at the final timestep. If write_ascii is enabled, the file suffix is .db. This is not written to netCDF!

Write $E_\parallel$ at the final timestep. If write_ascii is enabled, the file suffix is .epar

Write $\phi, A_\parallel, B_\parallel$ at the final timestep. If write_ascii is enabled, the file suffix is .fields

Write various moments (densities, parallel and perpendicular velocities and temperatures, and heat and momentum fluxes) at the final timestep. If write_ascii is enabled, the file suffix is .fields and contains the moments, their magnitudes, and field-line averages. The netCDF output has only the values.

Write instantaneous fluxes to output file every nwrite timesteps

Write fluxes (heat, momentum and particle; total and per-species) every nwrite timesteps.

If run is nonlinear, this defaults to true

Write fluxes (heat, momentum and particle; total and per-species) as a function of Fourier mode every nwrite timesteps.

If run is nonlinear, this defaults to true

Write moments (density, parallel flow, and parallel and perpendicular temperatures) in non-guiding centre coordinates every nwrite timesteps

Write $g(v_\parallel,v_\perp)$ at ik=it=is=1, ig=0 to text file <runname>.dist

Write $g$ as a function of real space every nmovie timesteps to text file ".yxdist"

Write out various heating, free energy and energy injection diagnostics. Text file extension is .heat

Write time averaged external current in the antenna, $\operatorname{Re}(k_\perp^2 A_\mathrm{antenna})$, as a function of $k_x, k_y$. File suffix is .jext

Calculates and writes the electrostatic drive of zonal flows every nwrite timesteps. The output kinetic_energy_transfer_theta resolves this over $\theta$ only. kinetic_energy_transfer_theta_kxsource, kinetic_energy_transfer_theta_kxtarget, and kinetic_energy_transfer_theta_kysource give additional insights by resolving over individual source or target scales.

Write the parallel spectrum of $\phi, A_\parallel, B_\parallel$ at final timestep. File suffix is .kpar

Print estimated frequencies and growth rates to text file every nwrite timesteps

Write antenna_w every nwrite timesteps

FIXME: Define antenna_w

Write the estimated maximum error from velocity space integrals for various quantities

Write various moments (total and non-adiabatic part of perturbed species density, perturbed parallel flow, perturbed parallel and perpendicular temperatures, parallel heat flux, particule flux and heat flux) every nwrite timesteps

Write the poloidal distributions of the fluxes of particles, parallel momentum, perpendicular momentum, and energy every nwrite timesteps.

See section 3.1 and appendix A of Ball et al. PPCF 58 (2016) 045023 as well as section 5 of "GS2 analytic geometry specification"

Write the whole total density moment every nwrite timesteps

Write time-averaged growth rate and frequency to the output text file every nwrite timesteps. Time average is rolling window over the previous navg timesteps

Write instantaneous growth rate and frequency every nwrite timesteps

Write parities in distribution and particle fluxes to text file with the suffix .parity

FIXME: Clarify what this means

Write the entire $\phi$ field every nwrite timesteps

Write a simple quasi-linear metric to netcdf.

Write the particle and momentum flux as a function of $\theta$ and velocity space. See gs2_diagnostics_knobs and gs2_diagnostics_knobs

Write the whole perturbed perpendicular temperature moment every nwrite timesteps

Write the whole perturbed parallel velocity moment every nwrite timesteps

Write estimates of error resulting from velocity space integrals in the calculation of various quantities every nwrite timesteps.

Write the transfer of free energy, $\tau$, as a function of $(k_x, k_y)$, averaged over $\theta$, every nwrite timesteps