diagnostics_base_config_type Derived Type

type, public, extends(abstract_config_type) :: diagnostics_base_config_type

Used to represent the input configuration of gs2_diagnostics. This is the version used by the original diagnostics module.


Contents


Components

Type Visibility Attributes Name Initial
logical, public :: exist = .false.

Does the related namelist exist in the target input file?

integer, public :: index = 0

Used to hold the specific index of numbered namelists

logical, public :: skip_read = .false.

Do we want to skip the read step in init?

logical, public :: skip_broadcast = .false.

Do we want to skip the broadcast step in init?

logical, public :: append_old = .false.

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

integer, public :: conv_max_step = 80000

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

integer, public :: conv_min_step = 4000

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

integer, public :: conv_nstep_av = 4000

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

integer, public :: conv_nsteps_converged = 10000

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

real, public :: conv_test_multiplier = 4e-1

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

logical, public :: dump_check1 = .false.

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

logical, public :: dump_check2 = .false.

Write out at igomega to <run name>.dc2.

logical, public :: dump_fields_periodically = .false.

Write out to dump.fields.t=(time) every 10 * nwrite timesteps.

logical, public :: enable_parallel = .false.

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.

logical, public :: exit_when_converged = .true.

Exit when the run has reached convergence

logical, public :: file_safety_check = .true.

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

integer, public :: igomega = 0

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

logical, public :: make_movie = .false.

Write out in real space over time, suitable for creating animations. Timestep period is controlled with nmovie

integer, public :: navg = 10

Number of timesteps to average over for time-averaged diagnostics

integer, public :: ncheck = 10

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

integer, public :: nc_sync_freq = 10

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.

integer, public :: nmovie = -1

Timestep period to write real space fields

integer, public :: nsave = -1

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

integer, public :: nwrite = 10

Timestep period for writing outputs

integer, public :: nwrite_mult = 10

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?

logical, public :: ob_midplane = .false.

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

real, public :: omegatinst = 1.0e6

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

real, public :: omegatol = 1e-3

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

More explicitly, the convergence criterion is:

where is averaged over the last navg timesteps.

logical, public :: print_flux_line = .false.

Print the instantaneous fluxes to screen/stdout every nwrite timesteps

logical, public :: print_line = .false.

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

logical, public :: save_distfn = .false.

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

logical, public :: save_for_restart = .false.

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

logical, public :: save_glo_info_and_grids = .false.

Save some layout and distribution information in restart files

logical, public :: save_many = .false.

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.

logical, public :: save_velocities = .false.

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

logical, public :: serial_netcdf4 = .false.

logical, public :: use_nonlin_convergence = .false.

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.

logical, public :: write_any = .true.

If .false., skip writing any diagnostics

logical, public :: write_apar_over_time = .false.

Write the entire field every nwrite timesteps

logical, public :: write_ascii = .true.

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

logical, public :: write_avg_moments = .false.

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

logical, public :: write_bpar_over_time = .false.

Write the entire field every nwrite timesteps

logical, public :: write_cerr = .false.

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

FIXME: What does this mean?

logical, public :: write_collisional = .false.

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

logical, public :: write_correlation = .true.

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

logical, public :: write_correlation_extend = .false.

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

logical, public :: write_cross_phase = .false.

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

logical, public :: write_density_over_time = .false.

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

logical, public :: write_eigenfunc = .false.

Write normalised to the value of at the outboard midplane every nwrite timesteps.

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

logical, public :: write_fields = .true.

Enable writing every nwrite timesteps

logical, public :: write_final_antot = .false.

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

logical, public :: write_final_db = .false.

Write at the final timestep. If write_ascii is enabled, the file suffix is .db

logical, public :: write_final_epar = .false.

Write at the final timestep. If write_ascii is enabled, the file suffix is .epar

logical, public :: write_final_fields = .false.

Write at the final timestep. If write_ascii is enabled, the file suffix is .fields

logical, public :: write_final_moments = .false.

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.

logical, public :: write_flux_line = .false.

Write instantaneous fluxes to output file every nwrite timesteps

logical, public :: write_fluxes = .false.

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

If run is nonlinear, this defaults to true

logical, public :: write_fluxes_by_mode = .false.

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

logical, public :: write_full_moments_notgc = .false.

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

logical, public :: write_g = .false.

Write at ik=it=is=1, ig=0 to text file <runname>.dist

logical, public :: write_gs = .false.

logical, public :: write_gyx = .false.

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

logical, public :: write_heating = .false.

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

logical, public :: write_jext = .false.

Write time averaged external current in the antenna, , as a function of . File suffix is .jext

logical, public :: write_kpar = .false.

Write the parallel spectrum of at final timestep. File suffix is .kpar

logical, public :: write_line = .true.

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

logical, public :: write_lorentzian = .false.

Write antenna_w every nwrite timesteps

FIXME: Define antenna_w

logical, public :: write_max_verr = .false.

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

logical, public :: write_moments = .true.

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

logical, public :: write_nl_flux_dist = .false.

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"

logical, public :: write_ntot_over_time = .false.

Write the whole total density moment every nwrite timesteps

logical, public :: write_omavg = .true.

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

logical, public :: write_omega = .true.

Write instantaneous growth rate and frequency every nwrite timesteps

logical, public :: write_parity = .false.

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

FIXME: Clarify what this means

logical, public :: write_pflux_sym = .false.

Write particle flux density as a function of and velocity space every nwrite timesteps. Used for looking at the effect of asymmetry. See Parra et al POP 18 062501 2011 and ask Jung-Pyo Lee

logical, public :: write_pflux_tormom = .false.

Write toroidal angular momentum flux carried by particle flux every nwrite timesteps. Only calculated if gs2 is built with LOWFLOW on.

logical, public :: write_phi_over_time = .false.

Write the entire field every nwrite timesteps

logical, public :: write_ql_metric = .true.

Write a simple quasi-linear metric to netcdf.

logical, public :: write_symmetry = .false.

Write the particle and momentum flux as a function of and velocity space. See write_pflux_sym and write_pflux_tormom

logical, public :: write_tperp_over_time = .false.

Write the whole perturbed perpendicular temperature moment every nwrite timesteps

logical, public :: write_upar_over_time = .false.

Write the whole perturbed parallel velocity moment every nwrite timesteps

logical, public :: write_verr = .false.

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

logical, public :: write_zonal_transfer = .false.

Write the transfer of free energy, , as a function of , averaged over , every nwrite timesteps


Type-Bound Procedures

procedure, public, :: is_initialised => is_initialised_generic

procedure, public, :: init => init_generic

  • private subroutine init_generic(self, name, requires_index, index)

    Fully initialise the config object

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(inout) :: self
    character(len=*), intent(in), optional :: name
    logical, intent(in), optional :: requires_index
    integer, intent(in), optional :: index

procedure, public, :: setup => setup_generic

  • private subroutine setup_generic(self, name, requires_index, index)

    Do some standard setup/checking

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(inout) :: self
    character(len=*), intent(in), optional :: name
    logical, intent(in), optional :: requires_index
    integer, intent(in), optional :: index

procedure, public, :: write_namelist_header

  • private subroutine write_namelist_header(self, unit)

    Write the namelist header for this instance

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(in) :: self
    integer, intent(in) :: unit

procedure, public, :: get_name => get_name_generic

  • private function get_name_generic(self)

    Returns the namelist name. Not very useful at the moment but may want to do more interesting things in the future

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(in) :: self

    Return Value character(len=CONFIG_MAX_NAME_LEN)

procedure, public, :: get_requires_index => get_requires_index_generic

  • private function get_requires_index_generic(self)

    Returns the requires_index value. Allows access whilst keeping the variable private

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(in) :: self

    Return Value logical

procedure, public, nopass :: write_namelist_footer

  • private subroutine write_namelist_footer(unit)

    Write the namelist footer

    Arguments

    Type IntentOptional Attributes Name
    integer, intent(in) :: unit
  • private subroutine write_key_val_string(key, val, unit)

    Writes a {key,val} pair where the value is of type character

    Arguments

    Type IntentOptional Attributes Name
    character(len=*), intent(in) :: key
    character(len=*), intent(in) :: val
    integer, intent(in) :: unit
  • private subroutine write_key_val_real(key, val, unit)

    Writes a {key,val} pair where the value is of type real

    Arguments

    Type IntentOptional Attributes Name
    character(len=*), intent(in) :: key
    real, intent(in) :: val
    integer, intent(in) :: unit
  • private subroutine write_key_val_complex(key, val, unit)

    Writes a {key,val} pair where the value is of type complex

    Arguments

    Type IntentOptional Attributes Name
    character(len=*), intent(in) :: key
    complex, intent(in) :: val
    integer, intent(in) :: unit
  • private subroutine write_key_val_integer(key, val, unit)

    Writes a {key,val} pair where the value is of type integer

    Arguments

    Type IntentOptional Attributes Name
    character(len=*), intent(in) :: key
    integer, intent(in) :: val
    integer, intent(in) :: unit
  • private subroutine write_key_val_logical(key, val, unit)

    Writes a {key,val} pair where the value is of type logical

    Arguments

    Type IntentOptional Attributes Name
    character(len=*), intent(in) :: key
    logical, intent(in) :: val
    integer, intent(in) :: unit
  • private subroutine write_key_val_real_array(self, key, val, unit)

    Writes a {key,val} pair where the value is of type real array

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(in) :: self
    character(len=*), intent(in) :: key
    real, intent(in), dimension(:) :: val
    integer, intent(in) :: unit
  • private subroutine write_key_val_complex_array(self, key, val, unit)

    Writes a {key,val} pair where the value is of type complex array

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(in) :: self
    character(len=*), intent(in) :: key
    complex, intent(in), dimension(:) :: val
    integer, intent(in) :: unit
  • private subroutine write_key_val_integer_array(self, key, val, unit)

    Writes a {key,val} pair where the value is of type integer array

    Arguments

    Type IntentOptional Attributes Name
    class(abstract_config_type), intent(in) :: self
    character(len=*), intent(in) :: key
    integer, intent(in), dimension(:) :: val
    integer, intent(in) :: unit

procedure, public :: read => read_diagnostics_base_config

procedure, public :: write => write_diagnostics_base_config

procedure, public :: reset => reset_diagnostics_base_config

procedure, public :: broadcast => broadcast_diagnostics_base_config

procedure, public, nopass :: get_default_name => get_default_name_diagnostics_base_config

procedure, public, nopass :: get_default_requires_index => get_default_requires_index_diagnostics_base_config

Source Code

  type, extends(abstract_config_type) :: diagnostics_base_config_type
    ! namelist : gs2_diagnostics_knobs
    ! indexed : false

    !> Append output data to a previous output file `<run name>.out.nc` if it
    !> already exists. Grid sizes must be unchanged.
    logical :: append_old = .false.
    !> Used for Trinity nonlinear convergence check
    !> ([[gs2_diagnostics_knobs:use_nonlin_convergence]]). The maximum number
    !> of time steps, after which consider the run converged regardless.
    integer :: conv_max_step = 80000
    !> Used for the Trinity nonlinear convergence check
    !> ([[gs2_diagnostics_knobs:use_nonlin_convergence]]). The minimum number
    !> of time steps before convergence condition can trigger an exit.
    integer :: conv_min_step = 4000
    !> Used for the Trinity nonlinear convergence check
    !> ([[gs2_diagnostics_knobs:use_nonlin_convergence]]). The number of
    !> timesteps the convergence condition averages over
    integer :: conv_nstep_av = 4000
    !> Used for the Trinity nonlinear convergence check
    !> ([[gs2_diagnostics_knobs:use_nonlin_convergence]]). The number of steps
    !> where convergence is true before convergence is accepted
    integer :: conv_nsteps_converged = 10000
    !> Used for the Trinity nonlinear convergence check
    !> ([[gs2_diagnostics_knobs:use_nonlin_convergence]]). Multiplier for the
    !> cumulative average of the heat flux
    real :: conv_test_multiplier = 4e-1
    !> Write out the field-line average of \(\phi\) to `dump.check1`. This option
    !> is usually used for Rosenbluth-Hinton calculations.
    !>
    !> @warning You probably don't want this?
    !>
    !> @warning Non-functional in new diagnostics
    logical :: dump_check1 = .false.
    !> Write out \(A_\parallel(k_x, k_y)\) at `igomega` to `<run name>.dc2`.
    !>
    !> @warning You probably don't want this?
    !>
    !> @warning Non-functional in new diagnostics
    logical :: dump_check2 = .false.
    !> Write out \(\phi, A_\parallel, B_\parallel\) to `dump.fields.t=(time)`
    !> every `10 * nwrite` timesteps.
    !>
    !> @warning You probably don't want this?  Expensive.
    logical :: dump_fields_periodically = .false.
    !> 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.
    !>
    !> @warning Only in new diagnostics
    logical :: enable_parallel = .false.
    !> Exit when the run has reached convergence
    logical :: exit_when_converged = .true.
    !> Verify that the restart file(s) can be written before starting the run
    logical :: file_safety_check = .true.
    !> 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.
    integer :: igomega = 0
    !> Write out \(\phi, A_\parallel, B_\parallel\) in real space over time,
    !> suitable for creating animations. Timestep period is controlled with
    !> [[gs2_diagnostics_knobs:nmovie]]
    !>
    !>
    !> @warning This option can write a lot of data! Consider doing the Fourier
    !> transforms of the fields in post-processing instead.
    !>
    !> @warning In new diagnostics, the timestep period is controlled with
    !> [[gs2_diagnostics_knobs:nwrite]]
    logical :: make_movie = .false.
    !> Number of timesteps to average over for time-averaged diagnostics
    !>
    !> @warning Default value differs between old (100) and new (10)
    !> diagnostics
    integer :: navg = 10
    !> FIXME: Timestep period of which to check velocity space resolution and
    !> correction by varying collisionality. But doesn't happen on timesteps
    !> when diagnostics are written.
    !>
    !> @warning Only in new diagnostics
    !>
    !> @warning This value "shadows" the `ncheck` input of the
    !> collisions namelist.
    integer :: ncheck = 10
    !> 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.
    integer :: nc_sync_freq = 10
    !> Timestep period to write real space fields \(\phi, A_\parallel,
    !> B_\parallel\)
    !>
    !> @warning Non-functional in new diagnostics. Instead use
    !> [[gs2_diagnostics_knobs:nwrite]]
    !>
    !> @warning Default value differs between old (1000) and new (-1)
    !> diagnostics
    integer :: nmovie = -1
    !> Timestep period for writing restart data if
    !> [[gs2_diagnostics_knobs:save_for_restart]] is `.true.`. Negative values
    !> disable the periodic checkpoints.
    integer :: nsave = -1
    !> Timestep period for writing outputs
    !>
    !> @warning Default value differs between old (`== 100`) and new (`== 10`)
    !> diagnostics!
    integer :: nwrite = 10
    !> 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?
    !>
    !> @warning Controls different diagnostics in new diagnostics
    integer :: nwrite_mult = 10
    !> If `.true.`, write moments at the outboard midplane only, as opposed to
    !> along the entire flux surface
    !>
    !> @warning Non-functional in new diagnostics
    !>
    !> @warning Default value differs between old (.true.) and new (.false.) diagnostics
    logical :: ob_midplane = .false.
    !> Threshold complex frequency (\(\Omega\)) for detecting a numerical
    !> instability. If \(\abs(\Omega)\) averaged over
    !> [[gs2_diagnostics_knobs:navg]] timesteps is greater than `omegatinst`,
    !> abort the run.
    !>
    !> @warning Default value differs between old (1.0) and new (1.0e6)
    !> diagnostics
    real :: omegatinst = 1.0e6
    !> Frequency (\(\omega\)) convergence tolerance. Consider the simulation
    !> converged and finish the run if \(\omega\) has changed by less than
    !> `omegatol` over the last [[gs2_diagnostics_knobs: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.
    real :: omegatol = 1e-3
    !> Print the instantaneous fluxes to screen/stdout every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    logical :: print_flux_line = .false.
    !> Print estimated frequencies and growth rates to screen/stdout every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Default value differs between old (`.true.`) and new
    !> (`.false.`) diagnostics
    logical :: print_line = .false.
    !> Write the distribution function to `<rootname>.nc.dfn.<processor>`
    !> files. Only written at end of simulation
    logical :: save_distfn = .false.
    !> Write restart files at the end of the simulation. If
    !> [[gs2_diagnostics_knobs:nsave]] is positive, then also enable
    !> checkpoints by writing restart files every `nsave` timesteps.
    logical :: save_for_restart = .false.
    !> Save some layout and distribution information in restart files
    logical :: save_glo_info_and_grids = .false.
    !> 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
    !> [[init_g_knobs:read_many]] in order to restart from multiple files.
    logical :: save_many = .false.
    !> Save parallel and perpendicular velocities in final restart and/or
    !> distribution function files
    logical :: save_velocities = .false.
    !> @warning Not used
    !>
    !> @warning Only in new diagnostics
    logical :: serial_netcdf4 = .false.
    !> 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 [[gs2_diagnostics_knobs:conv_test_multiplier]],
    !> [[gs2_diagnostics_knobs:conv_nsteps_converged]],
    !> [[gs2_diagnostics_knobs:conv_nsteps_av]],
    !> [[gs2_diagnostics_knobs:conv_max_step]], and
    !> [[gs2_diagnostics_knobs:conv_min_step]].
    logical :: use_nonlin_convergence = .false.
    !> If `.false.`, skip writing any diagnostics
    !>
    !> @warning Only in new diagnostics
    !>
    !> @warning This also turns off checking the linear convergence
    logical :: write_any = .true.
    !> Write the entire \(A_\parallel\) field every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning New diagnostics requires
    !> [[gs2_diagnostics_knobs:write_fields]] to also be `.true.`
    !> (the default) to enable this
    logical :: write_apar_over_time = .false.
    !> 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
    logical :: write_ascii = .true.
    !> Write flux surface averaged low-order moments of \(g\) every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Prints a warning that this is ignored unless
    !> `grid_option==box`, but this doesn't appear to be the case?
    logical :: write_avg_moments = .false.
    !> Write the entire \(B_\parallel\) field every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning New diagnostics requires
    !> [[gs2_diagnostics_knobs:write_fields]] to also be `.true.`
    !> (the default) to enable this
    logical :: write_bpar_over_time = .false.
    !> Write the collision error every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps to text file with suffix `.cres`
    !>
    !> FIXME: What does this mean?
    !>
    !> @warning In new diagnostics, only writes to ascii
    !>
    !> @warning This is expensive
    logical :: write_cerr = .false.
    !> Write collisional heating (collisional and hyper viscous rate of loss of
    !> free energy for each mode) every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps
    !>
    !> @warning Only in new diagnostics
    logical :: write_collisional = .false.
    !> Write two point parallel correlation function calculated from the
    !> electric potential as a function of \(k_y\) and parallel separation
    !> every [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Default value differs between old (`.false.`) and new
    !> (`.true.`) diagnostics
    logical :: write_correlation = .true.
    !> 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
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps once istep > nstep/4.
    !>
    !> @warning This diagnostic can have large persistent memory cost.
    logical :: write_correlation_extend = .false.
    !> Write the cross phase between electron density and perpendicular
    !> electron temperature every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps. Calculated at both the outboard midplane, averaged across
    !> \(x\) and \(y\); and averaged across all space
    !>
    !> @warning In old diagnostics, only written to text files
    logical :: write_cross_phase = .false.
    !> Write the whole non-adiabatic part of the density moment every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Requires [[gs2_diagnostics_knobs:write_moments]] to also be
    !> `.true.`
    !>
    !> @warning Only in new diagnostics
    logical :: write_density_over_time = .false.
    !> Write \(\phi, A_\parallel, B_\parallel\) normalised to the value of
    !> \(\phi\) at the outboard midplane every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps.
    !>
    !> If [[gs2_diagnostics_knobs:write_ascii]] is enabled, the text file is
    !> `<runname>.eigenfunc`.
    !>
    !> @note The normalising factor for a given \((\theta, k_y)\) point may not
    !> be exactly \(\phi\) at the outboard midplane if this value is zero
    !> there. If the adjacent point in \(\theta\) is also zero, then the fields
    !> will be unnormalised at that \((\theta, k_y)\).
    !>
    !> @warning If this option is turned on, the same normalising factor will
    !> also be used for the text output in
    !> [[gs2_diagnostics_knobs:write_final_moments]]
    !>
    !> @warning In old diagnostics, this is only done on exit, not every
    !> `nwrite` timesteps!
    !>
    !> @warning The text output is normalised (see note above), but the netCDF
    !> output is not
    logical :: write_eigenfunc = .false.
    !> Enable writing \(\phi, A_\parallel, B_\parallel\) every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning In old diagnostics, this only writes them on exit and
    !> [[gs2_diagnostics_knobs:write_phi_over_time]],
    !> [[gs2_diagnostics_knobs:write_apar_over_time]] and
    !> [[gs2_diagnostics_knobs:write_bpar_over_time]] instead control writing
    !> the fields over time, respectively. In new diagnostics, this will disable
    !> writing all three fields if set to `.false.`
    !>
    !> @warning Default value differs between old (`.false.`) and new
    !> (`.true.`) diagnostics
    logical :: write_fields = .true.
    !> Write the right-hand sides of the field equations at the final
    !> timestep. If [[gs2_diagnostics_knobs:write_ascii]] is enabled, the file
    !> suffix is `.antot`
    !>
    !> @warning In new diagnostics, this is not written to netCDF!
    logical :: write_final_antot = .false.
    !> Write \(\delta B\) at the final timestep. If
    !> [[gs2_diagnostics_knobs:write_ascii]] is enabled, the file suffix is
    !> `.db`
    !>
    !> @warning In new diagnostics, this is not written to netCDF!
    logical :: write_final_db = .false.
    !> Write \(E_\parallel\) at the final timestep. If
    !> [[gs2_diagnostics_knobs:write_ascii]] is enabled, the file suffix is
    !> `.epar`
    !>
    !> @warning In new diagnostics, this is not written to netCDF!
    logical :: write_final_epar = .false.
    !> Write \(\phi, A_\parallel, B_\parallel\) at the final timestep. If
    !> [[gs2_diagnostics_knobs:write_ascii]] is enabled, the file suffix is
    !> `.fields`
    !>
    !> @warning In new diagnostics, this is not written to netCDF!
    logical :: write_final_fields = .false.
    !> Write various moments (densities, parallel and perpendicular
    !> velocities and temperatures, and heat and momentum fluxes) at
    !> the final timestep. If [[gs2_diagnostics_knobs: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.
    !>
    !> @warning If [[gs2_diagnostics_knobs:write_eigenfunc]] is
    !> enabled, then the same normalising factor is used for the
    !> final moments. Otherwise, the moments are unnormalised.
    !>
    !> @warning In new diagnostics, this is not written to netCDF!
    !>
    !> @warning The text output is normalised (see note above), but
    !> the netCDF output is not
    logical :: write_final_moments = .false.
    !> Write instantaneous fluxes to output file every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Output formats and quantities differ between old and new
    !> diagnostics
    logical :: write_flux_line = .false.
    !> Write fluxes (heat, momentum and particle; total and per-species) every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps.
    !>
    !> If run is nonlinear, this defaults to true
    !>
    !> @warning In old diagnostics, this also turns on `write_fluxes_by_mode`
    logical :: write_fluxes = .false.
    !> Write fluxes (heat, momentum and particle; total and per-species) as a
    !> function of Fourier mode every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps.
    !>
    !> If run is nonlinear, this defaults to true
    !>
    !> @warning In old diagnostics, this is combined with `write_fluxes`
    logical :: write_fluxes_by_mode = .false.
    !> Write moments (density, parallel flow, and parallel and perpendicular
    !> temperatures) in non-guiding centre coordinates every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    logical :: write_full_moments_notgc = .false.
    !> Write \(g(v_\parallel,v_\perp)\) at `ik=it=is=1, ig=0` to text file
    !> `<runname>.dist`
    !>
    !> @warning Only to text files
    logical :: write_g = .false.
    !> FIXME: Add documentation
    !>
    !> @warning Only outputs to text files
    logical :: write_gs = .false.
    !> Write \(g\) as a function of real space every
    !> [[gs2_diagnostics_knobs:nmovie]] timesteps to text file
    !> "<runname>.yxdist"
    !>
    !> @warning Only to text files
    logical :: write_gyx = .false.
    !> Write out various heating, free energy and energy injection
    !> diagnostics. Text file extension is `.heat`
    logical :: write_heating = .false.
    !> 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`
    !>
    !> @warning Only in new diagnostics
    logical :: write_jext = .false.
    !> Write the parallel spectrum of \(\phi, A_\parallel,
    !> B_\parallel\) at final timestep. File suffix is `.kpar`
    !>
    !> @warning Output only to text files
    logical :: write_kpar = .false.
    !> Print estimated frequencies and growth rates to text file every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    logical :: write_line = .true.
    !> Write `antenna_w` every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps
    !>
    !> FIXME: Define `antenna_w`
    !>
    !> @warning Old diagnostics only writes to text files
    !>
    !> @warning New diagnostics only writes to netCDF
    logical :: write_lorentzian = .false.
    !> Write the estimated maximum error from velocity space
    !> integrals for various quantities
    !>
    !> @warning Old diagnostics only outputs to text file
    logical :: write_max_verr = .false.
    !> 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
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Only outputs to netCDF files
    !>
    !> @warning New diagnostics writes various averages of the moments. To get
    !> the same output as old diagnostics, **also** set
    !> [[gs2_diagnostics_knobs:write_ntot_over_time]],
    !> [[gs2_diagnostics_knobs:write_density_over_time]],
    !> [[gs2_diagnostics_knobs:write_upar_over_time]],
    !> [[gs2_diagnostics_knobs:write_tperp_over_time]] to `.true.`
    !>
    !> @warning Default value differs between old (`.false.`) and new
    !> (`.true.`) diagnostics
    logical :: write_moments = .true.
    !> Write the poloidal distributions of the fluxes of particles,
    !> parallel momentum, perpendicular momentum, and energy every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps.
    !>
    !> See section 3.1 and appendix A of [Ball et al. PPCF 58 (2016)
    !> 045023](https://doi.org/10.1088/0741-3335/58/4/045023) as well as
    !> section 5 of "GS2 analytic geometry specification"
    logical :: write_nl_flux_dist = .false.
    !> Write the whole total density moment every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Requires [[gs2_diagnostics_knobs:write_moments]] to also be
    !> `.true.`
    !>
    !> @warning Only in new diagnostics
    logical :: write_ntot_over_time = .false.
    !> Write time-averaged growth rate and frequency to the output text file
    !> every [[gs2_diagnostics_knobs:nwrite]] timesteps. Time average is
    !> rolling window over the previous [[gs2_diagnostics_knobs:navg]]
    !> timesteps
    !>
    !> @warning Non-functional in new diagnostics, time-average is also written
    !> with [[gs2_diagnostics_knobs:write_omega]] instead
    logical :: write_omavg = .true.
    !> Write instantaneous growth rate and frequency every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Old diagnostics only writes to output text file
    !>
    !> @warning New diagnostics only writes to netCDF file
    !>
    !> @warning New diagnostics also writes time-average with this
    !> option. Output is the complex frequency, rather than separate growth
    !> rate and real frequency
    logical :: write_omega = .true.
    !> Write parities in distribution and particle fluxes to text file with the
    !> suffix `.parity`
    !>
    !> FIXME: Clarify what this means
    logical :: write_parity = .false.
    !> Write particle flux density as a function of \(\theta\) and velocity
    !> space every [[gs2_diagnostics_knobs:nwrite]] timesteps. Used for looking
    !> at the effect of asymmetry. See [Parra et al POP 18 062501
    !> 2011](https://doi.org/10.1063/1.3586332) and ask Jung-Pyo Lee
    !>
    !> @warning Only outputs to netCDF
    !>
    !> @warning Non-functional in new diagnostics, use
    !> [[gs2_diagnostics_knobs:write_symmetry]] instead
    logical :: write_pflux_sym = .false.
    !> Write toroidal angular momentum flux carried by particle flux every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps. Only calculated if `gs2` is
    !> built with `LOWFLOW` on.
    !>
    !> @warning Only outputs to netCDF
    !>
    !> @warning Non-functional in new diagnostics
    logical :: write_pflux_tormom = .false.
    !> Write the entire \(\phi\) field every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps
    !>
    !> @warning New diagnostics requires
    !> [[gs2_diagnostics_knobs:write_fields]] to also be `.true.`
    !> (the default) to enable this
    logical :: write_phi_over_time = .false.
    !> Write a simple quasi-linear metric to netcdf.
    logical :: write_ql_metric = .true.
    !> Write the particle and momentum flux as a function of \(\theta\) and
    !> velocity space. See [[gs2_diagnostics_knobs:write_pflux_sym]] and
    !> [[gs2_diagnostics_knobs:write_pflux_tormom]]
    !>
    !> @warning Only outputs to netCDF
    !>
    !> @warning Old diagnostics does not write the particle flux, use
    !> [[gs2_diagnostics_knobs:write_pflux_sym]] instead
    logical :: write_symmetry = .false.
    !> Write the whole perturbed perpendicular temperature moment every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Requires [[gs2_diagnostics_knobs:write_moments]] to also be
    !> `.true.`
    !>
    !> @warning Only in new diagnostics
    logical :: write_tperp_over_time = .false.
    !> Write the whole perturbed parallel velocity moment every
    !> [[gs2_diagnostics_knobs:nwrite]] timesteps
    !>
    !> @warning Requires [[gs2_diagnostics_knobs:write_moments]] to also be
    !> `.true.`
    !>
    !> @warning Only in new diagnostics
    logical :: write_upar_over_time = .false.
    !> Write estimates of error resulting from velocity space integrals in the
    !> calculation of various quantities every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps.
    !>
    !> @warning Output only to text file
    !>
    !> @warning New diagnostics also writes to netCDF every
    !> [[gs2_diagnostics_knobs:ncheck]] timesteps, along with some other
    !> quantities such as collisionality
    !>
    !> @warning This is expensive
    logical :: write_verr = .false.
    !> Write the transfer of free energy, \(\tau\), as a function of \((k_x,
    !> k_y)\), averaged over \(\theta\), every [[gs2_diagnostics_knobs:nwrite]]
    !> timesteps
    !>
    !> @warning Only in new diagnostics
    logical :: write_zonal_transfer = .false.
  contains
    procedure, public :: read => read_diagnostics_base_config
    procedure, public :: write => write_diagnostics_base_config
    procedure, public :: reset => reset_diagnostics_base_config
    procedure, public :: broadcast => broadcast_diagnostics_base_config
    procedure, public, nopass :: get_default_name => get_default_name_diagnostics_base_config
    procedure, public, nopass :: get_default_requires_index => get_default_requires_index_diagnostics_base_config
  end type diagnostics_base_config_type