HYDRAD Configuration Parameters

The tables below give an exhaustive list of all of the different HYDRAD configuration options. If the units are listed, the input must have units that can be converted to the listed unit with the Astropy units module, e.g. loop_length can be input in Mm.

General

Name	Description	Type	Units
total_time	Total duration of the simulation	float	s
output_interval	How often results are printed to file	float	s
loop_length	Footpoint-to-footpoint distance of the coronal loop	float	cm
loop_inclination	Angle between loop and surface normal	float	degree
footpoint_height	Length of the chromosphere	float	cm
poly_fit_gravity	Configuration parameters for the piecewise polynomial fit to the gravitational profile	dict
poly_fit_magnetic_field	Configuration parameters for the piecewise polynomial fit to the magnetic field profile	dict
logging_frequency	Frequency (in number of timesteps) that progress is printed to the screen	int
initial_amr_file	Adaptive mesh file to initialize loop from; if not given, uses the result from the initial conditions code	str
write_file_physical	Toggle writing .phy solutions file	bool
write_file_ion_populations	Toggle writing .ine file	bool
write_file_hydrogren_level_populations	Toggle writing .hstate file	bool
write_file_timescales	Toggle writing .scl file	bool
write_file_equation_terms	Toggle writing .trm file	bool
heat_flux_limiting_coefficient	See Eq. A15 of BC13	float
heat_flux_timestep_limit	Minimum value the heat flux will limit timestep to	float	s
use_kinetic_model	Toggle using the kinetic model for the heat flux	bool
minimum_collisional_coupling_timescale		float	s
force_single_fluid	If true, force electron and ion quantities to be equal	bool
use_openmp	If true, parallelize over threads with OpenMP. This option is most useful when including a NLTE chromosphere.	bool
grid_cells_per_thread	If using OpenMP parallelization, approximate number of grid cells assigned to each thread	int
open_field	If true, one footpoint is assumed to not connect to the surface	bool
force_symmetry		bool

The poly_fit_gravity and poly_fit_magnetic_field entries are both dictionaries and must contain the following keys,

Name	Description	Type	Units
x	Spatial coordinate of the profile	array-like	cm
y	Profile, either gravity or magnetic field	array-like	cm s\(-2\) or G
domains	Left and right edges, in normalized spatial coordinates, over which to perform the fit. If fitting a single polynomial over the entire domain, this can just be [0,1].	array-like
order	Order of the polynomial fit	int

Initial Conditions

Name	Description	Type	Units
footpoint_temperature	Temperature at the loop footpoints	float	K
footpoint_density	Density at the loop footpoints	float	cm\(^{-3}\)
heating_location	Loop coordinate where heating is deposited to get equilibrium solution	float	cm
heating_scale_height	Spatial scale of heating to get equilibrium solution	float	cm
isothermal	If true, initial temperature profile is uniform	bool
heating_range_lower_bound	Lower bound on rate search range	float	erg cm\(^{-3}\) s\(^{-1}\)
heating_range_upper_bound	Upper bound on rate search range	float	erg cm\(^{-3}\) s\(^{-1}\)
heating_range_step_size	Resolution of heating rate search range	float
heating_range_fine_tuning		float
use_poly_fit_gravity	If true, use polynomial fit to gravitational profile when calculating initial conditions	bool
use_poly_fit_magnetic_field	If true, use polynomial fit to magnetic field profile when calculating initial conditions	bool

Heating

Name	Description	Type
electron_heating	Fraction of energy partitioned to the electrons. If 1, all of the heat is deposited in the electrons. If 0, all of the heat is deposited in the ions.	float
beam	Toggle beam heating model	bool
alfven_wave	Toggle Alfvèn wave heating model (experimental)	bool
background	Parameters for configuring the background heating	dict
events	List of properties for each heating event.	list

The background entry can have the following keys. If use_initial_conditions is set to True, none of the other keys need be included

Name	Description	Type	Units
use_initial_conditions	If true, use the heating parameters from the initial conditions and the computed equilibrium heating rate; if true, all other background heating parameters are ignored.	bool
location	Location of the energy deposition	float	cm
scale_height	Spatial scale of the energy deposition	float	cm
rate	Peak heating rate of the Gaussian heating profile	float	erg cm\(^{-3}\) s\(^{-1}\)

Each entry in the events list should be a dictionary with the following seven keys (and appropriate units) corresponding to each heating event. If the list is empty, it is assumed that the loop is not subject to any heating events.

Name	Description	Type	Units
time_start	The starting time in the simulation of a given heating event	float	s
rise_duration	The duration it takes to increase from the background heating rate to peak heating rate	float	s
decay_duration	The duration it takes to decrease from peak heating rate back to the background heating rate	float	s
total_duration	The total duration of the heating event. The time profile of the event is trapezoidal in shape.	float	s
location	The location along the loop where the heating event is centered. Must have a value between 0 and the total loop length.	float	cm
scale_height	The spatial width (Gaussian) of the heating event.	float	cm
rate	The peak heating rate of the heating event	float	erg cm\(^{-3}\) s\(^{-1}\)

Radiation

Name	Description	Type	Units
use_power_law_radiative_losses	If true, use piecewise power-law to calculate radiative losses	bool
lookup_table	Path (relative to the root of the HYDRAD directory) to lookup table for radiative losses. Ignored unless use_power_law_radiative_losses is also set.	str
decouple_ionization_state_solver	If true, the non-equilibrium population fractions are not fed back into the radiative loss calculation. This option will be ignored unless a list of elements is also passed to elements_nonequilibrium. If use_power_law_radiative_losses is false, the equilibrium population fractions will be used to calculate the radiative losses.	bool
density_dependent_rates	If true, uses density-dependent ionization/recombination rates from the ADAS database.	bool
optically_thick_radiation	If true, include optically thick lines in radiative losses	bool
nlte_chromosphere	Treat the chromosphere as being in non-local thermodynamic equilibrium. NOTE: This may significantly increase the computation time.	bool
minimum_density_limit	Density floor of the corona. This option is required if nlte_chromosphere is true.	float	cm\(^{-3}\)
ranges_dataset	Temperature and density ranges dataset	str
emissivity_dataset	Name of emissivity dataset	str
abundance_dataset	Name of abundance dataset	str
rates_dataset	Name of ionization/recombination dataset	str
elements_equilibrium	Elements for which the population fractions will be calculated assuming ionization equilibrium	list
elements_nonequilibrium	Elements for which the time-dependent, non-equilibrium population fractions will be calculated	list

In the lists of equilibrium and non-equilibrium elements, each entry can either be the atomic symbol, number, or the element name. As an example, each entry in the list below (which includes hydrogen, helium, carbon, and iron) is a valid element identifier,

elements = ['hydrogen', 'He', 'c', 26]

Solver

Name	Description	Type	Units
epsilon		float
safety_radiation	A multiplicative factor applied to the radiative timescale. Should be strictly greater than 0 and less than or equal to 1.	float
safety_conduction	A multiplicative factor applied to the conductive timescale. Should be strictly greater than 0 and less than or equal to 1.	float
safety_advection	A multiplicative factor applied to the advective timescale. Should be strictly greater than 0 and less than or equal to 1.	float
safety_atomic	A multiplicative factor applied to the atomic timescale. Should be strictly greater than 0 and less than or equal to 1.	float
safety_viscosity	A multiplicative factor applied to the viscous timescale. Should be strictly greater than 0 and less than or equal to 1.	float
cutoff_ion_fraction	Population fractions below this value are set to 0	float
epsilon_d	Safety factor for ion population solver; see B09	float
epsilon_r	Safety factor for ion population solver; see B09	float
timestep_increase_limit	Allowed fractional difference (between 0 and 1) between consecutive timesteps	float
relative_viscous_timescale		float
minimum_radiation_temperature		float	K
zero_over_temperature_interval	Temperature interval over which the chromospheric radiative losses are set to zero	float	K
minimum_temperature	Minimum allowed temperature in the grid	float	K
maximum_optically_thin_density		float	cm\(^{-3}\)
cutoff_temperature_fraction	Ratio between cutoff temperature and peak temperature. If set, use the method of JB19 to model the transition region.	float

Grid

Name	Description	Type	Units
adapt	Toggle using adaptive mesh refinement	bool
adapt_every_n_time_steps	How often to adapt on timestep	int
maximum_cell_width	The maximum allowed width of any grid cell	float	cm
maximum_refinement_level	The maximum number of times a grid cell can be split; see BC13	int
minimum_cells	Minimum allowed number of grid cells. If this is not set explicitly, it is calculated as \(n_{min}=\lceil L/\Delta s_{max}\rceil\), where \(L\) is the loop length and \(\Delta s_{max}\) is the maximum allowed grid cell width.	int
maximum_cells	Maximum allowed number of grid cells. If this is not set explicitly, \(n_{max}=\lfloor 2^{L_R}n_{min}\rfloor\), where \(L_R\) is the maximum refinement level and \(n_{min}\) is the minimum allowed number of grid cells.	int
minimum_delta_s	Smallest allowed grid cell width in the initial setup	float	cm
maximum_variation		float
refine_on_density	Use spatial variations in density to adaptively refine the grid	bool
refine_on_electron_energy	Use spatial variations in the electron energy to adaptively refine the grid	bool
refine_on_hydrogen_energy	Use spatial variations in the hydrogen energy to adaptively refine the grid	bool
minimum_fractional_difference	Minimum allowed difference (between 0 and 1) between adjacent cells	float
maximum_fractional_difference	Maximum allowed difference (between 0 and 1) between adjacent cells	float
linear_restriction	Use linear interpolation only	bool
enforce_conservation	Check whether energy has been conserved (i.e. correct numerical errors)	bool