diagnostics_base_config Module



Contents


Derived Types

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.

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.

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logical, public :: dump_check2 = .false.

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

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logical, public :: dump_fields_periodically = .false.

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

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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.

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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

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integer, public :: navg = 10

Number of timesteps to average over for time-averaged diagnostics

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integer, public :: ncheck = 10

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

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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

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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

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integer, public :: nwrite_mult = 10

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

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logical, public :: ob_midplane = .false.

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

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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.

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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.

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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

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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.

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logical, public :: save_velocities = .false.

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

logical, public :: serial_netcdf4 = .false.

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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

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logical, public :: write_apar_over_time = .false.

Write the entire field every nwrite timesteps

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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.

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logical, public :: write_avg_moments = .false.

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

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logical, public :: write_bpar_over_time = .false.

Write the entire field every nwrite timesteps

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logical, public :: write_cerr = .false.

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

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logical, public :: write_collisional = .false.

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

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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

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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.

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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

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logical, public :: write_density_over_time = .false.

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

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logical, public :: write_eigenfunc = .false.

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

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logical, public :: write_fields = .true.

Enable writing every nwrite timesteps

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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

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logical, public :: write_final_db = .false.

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

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logical, public :: write_final_epar = .false.

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

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logical, public :: write_final_fields = .false.

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

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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.

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logical, public :: write_flux_line = .false.

Write instantaneous fluxes to output file every nwrite timesteps

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logical, public :: write_fluxes = .false.

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

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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.

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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

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logical, public :: write_gs = .false.

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logical, public :: write_gyx = .false.

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

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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

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logical, public :: write_kpar = .false.

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

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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

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logical, public :: write_max_verr = .false.

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

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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

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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.

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logical, public :: write_ntot_over_time = .false.

Write the whole total density moment every nwrite timesteps

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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

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logical, public :: write_omega = .true.

Write instantaneous growth rate and frequency every nwrite timesteps

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logical, public :: write_parity = .false.

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

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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

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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.

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logical, public :: write_phi_over_time = .false.

Write the entire field every nwrite timesteps

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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

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logical, public :: write_tperp_over_time = .false.

Write the whole perturbed perpendicular temperature moment every nwrite timesteps

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logical, public :: write_upar_over_time = .false.

Write the whole perturbed parallel velocity moment every nwrite timesteps

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logical, public :: write_verr = .false.

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

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logical, public :: write_zonal_transfer = .false.

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

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Type-Bound Procedures

procedure , public , :: is_initialised => is_initialised_generic Function
procedure , public , :: init => init_generic Subroutine
procedure , public , :: setup => setup_generic Subroutine
procedure , public , :: write_namelist_header Subroutine
procedure , public , :: get_name => get_name_generic Function
procedure , public , :: get_requires_index => get_requires_index_generic Function
procedure , public , nopass :: write_namelist_footer Subroutine
generic, public , :: write_key_val => write_key_val_string, write_key_val_real, write_key_val_complex, write_key_val_integer, write_key_val_logical, write_key_val_real_array, write_key_val_complex_array, write_key_val_integer_array
procedure , public :: read => read_diagnostics_base_config Subroutine
procedure , public :: write => write_diagnostics_base_config Subroutine
procedure , public :: reset => reset_diagnostics_base_config Subroutine
procedure , public :: broadcast => broadcast_diagnostics_base_config Subroutine
procedure , public , nopass :: get_default_name => get_default_name_diagnostics_base_config Function
procedure , public , nopass :: get_default_requires_index => get_default_requires_index_diagnostics_base_config Function

Functions

Gets the default name for this namelist

Arguments

None

Return Value character(len=CONFIG_MAX_NAME_LEN)

Gets the default requires index for this namelist

Arguments

None

Return Value logical


Subroutines

public subroutine warn_about_nonfunctional_selection(diagnostic_switch, name)

Prints a warning about a non-functional diagnostic

Arguments

Type IntentOptional Attributes Name
logical, intent(in) :: diagnostic_switch

Diagnostic switch

character(len=*), intent(in) :: name

Name of the switch

public subroutine warn_about_deprecated_option(old_switch, old_name, new_switch, new_name)

Arguments

Type IntentOptional Attributes Name
logical, intent(in) :: old_switch

Deprecated diagnostic switch

character(len=*), intent(in) :: old_name

Deprecated name of the switch

logical, intent(inout) :: new_switch

New diagnostic switch

character(len=*), intent(in) :: new_name

New name of the switch

public subroutine read_diagnostics_base_config(self)

Reads in the gs2_diagnostics_knobs namelist and populates the member variables

Arguments

Type IntentOptional Attributes Name
class(diagnostics_base_config_type), intent(inout) :: self

public subroutine write_diagnostics_base_config(self, unit)

Writes out a namelist representing the current state of the config object

Arguments

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

public subroutine reset_diagnostics_base_config(self)

Resets the config object to the initial empty state

Arguments

Type IntentOptional Attributes Name
class(diagnostics_base_config_type), intent(inout) :: self

public subroutine broadcast_diagnostics_base_config(self)

Broadcasts all config parameters so object is populated identically on all processors

Arguments

Type IntentOptional Attributes Name
class(diagnostics_base_config_type), intent(inout) :: self