Parameter options

The parameter file allows for a full customisation of all Legolas variables. Lots of these variables have default values, except for the ones you have to set. These are initialised using a Fortran ieee_quiet_nan, propagating the value during setup. Legolas explicitly checks for nonsense values and will warn you if something is not right. This not only includes checks on improperly set variables but also on errors when setting the equilibrium: if you’re dividing by zero somewhere, for example, Legolas with catch it.

Note: Variables that have no default value must be set either through the parfile or in an equilibrium submodule. For the geometry, x_start and x_end variables we recommend setting these in a submodule.

You can create the parfile manually using this guide, or let Pylbo take care of generating one. More information on generating parfiles with Pylbo can be found here.

Gridlist

This namelist includes all grid-related variables.

Warning: For cylindrical geometries we override the start value with r = 0.025 if it is initialised with zero. Having r = 0 does not give issues per se but can introduce spurious eigenvalues: some matrix elements divide by $r^2$, which is not zero but corresponds to the first point in the Gaussian grid (which is very small) and can hence yield huge values in the A-matrix. You can force r = 0 through force_r0 = .true. in the gridlist, but this is not recommended.

Parameter Type Description Default value
geometry string geometry of the setup, "Cartesian" or "cylindrical" "" (must be set)
x_start real start of the grid NaN (must be set)
x_end real end of the grid NaN (must be set)
gridpoints int base number of gridpoints to use 31
force_r0 logical forces r=0 in cylindrical geometry .false.
mesh_accumulation logical uses mesh accumulation based on two Gaussian integrals .false.
ev_1 real expected value of the first Gaussian integral (only used with mesh accumulation) 1.25
sigma_1 real sigma of the first Gaussian integral (only used with mesh accumulation) 1.25
ev_2 real expected value of the second Gaussian integral (only used with mesh accumulation) 1.25
sigma_2 real sigma of the second Gaussian integral (only used with mesh accumulation) 1.25

equilibriumlist

This namelist includes all equilibrium-related variables.

Note: The parameter boundary_type only has one allowed value for the moment ("wall"), additional possibilities will be added in future versions.

Warning: The parameter remove_spurious_eigenvalues is really not recommended and should only be used as a last resort. Keeping r = 0.025 in cylindrical geometry usually solves all related issues you may have.

Parameter Type Description Default value
equilibrium_type string the equilibrium configuration to use, see the various options "adiabatic_homo"
boundary_type string boundary conditions to use "wall"
use_defaults logical if .true., uses the default values in the equilibrium submodule .true.
remove_spurious_eigenvalues logical removes the outer nb_spurious_eigenvalues purely real eigenvalues from the spectrum .false.
nb_spurious_eigenvalues int number of purely real eigenvalues to remove on each side of the imaginary axis 1

physicslist

This namelist includes all physics-related variables.

Note: If you use the default submodule values through use_default = .true., variables like radiative_cooling and resistivity (and related ones) are set in the submodules themselves. It’s good practice to set them in the submodule instead of through the parfile. The parfile functionality for these variables is provided for possible parameter studies, to prevent having to recompile the submodule over and over again.

Parameter Type Description Default value
mhd_gamma real the value for the ratio of specific heats gamma 5/3
flow logical if .true. flow is included .false.
radiative_cooling logical if .true. optically thin radiative losses are included .false.
ncool int amount of points used to interpolate the cooling curve 4000
cooling_curve string cooling curve to use, options are "jc_corona", "dalgarno", "ml_solar", "spex", "spex_dalgarno" and "rosner" "jc_corona"
external_gravity logical if .true. external gravity is included .false.
thermal_conduction logical if .true. thermal conduction is included .false.
use_fixed_tc_para logical if .true., uses a constant value for parallel conduction .false.
fixed_tc_para_value real constant value to use if use_fixed_tc_para = .true. 0.0
use_fixed_tc_perp logical if .true., uses a constant value for perpendicular conduction .false.
fixed_tc_perp_value real constant value to use if use_fixed_tc_perp = .true. 0.0
resistivity logical if .true. resistivity is included .false.
use_fixed_resistivity logical if .true., uses a constant value for the resistivity .false.
fixed_eta_value real constant value to use if use_fixed_resistivity = .true. 0.0
use_eta_dropoff logical if .true., smoothly drops off the resistivity profile to zero near the edges using a hyperbolic tangent profile .false.
dropoff_edge_dist real distance between grid edge and the smoothened profile center 0.05
dropoff_width real sets the width over which the profile is smoothened out 0.1

solvelist

This namelist includes all solver-related variables. For more information, see Solvers

Parameter Type Description Default value
solver string which solver to use "QR-invert"
arpack_mode string the mode for ARPACK, only used if solver="arnoldi" "standard"
number_of_eigenvalues int number of eigenvalues to calculate, only used if solver="arnoldi" 10
which eigenvalues string which eigenvalues to calculate, only used if solver="arnoldi" "LM"
maxiter int the maximum number of iterations the Arnoldi solver may take, only used if solver="arnoldi" 10N
sigma complex sigma-value around which to do shift-invert, only for arpack_mode="shift-invert" NaN

unitslist

This namelist includes all units-related variables.

Note: You can set the unit normalisations in the submodule as well. You can either supply unit_density or unit_temperature, but not both. See Units for more information.

Parameter Type Description Default value
cgs_units logical if .true. cgs normalisations are used .true.
unit_density real sets the unit density N/A (we use temperature instead)
unit_temperature real sets the unit temperature $10^6$ K
unit_magneticfield real sets the unit magnetic field $10$ Gauss
unit_length real sets the unit length $ 10^9$ cm

savelist

This namelist includes all variables related to data output.

Note: Legolas uses a logging-based system to write information to the console, similar to Python’s logging module. The level of output is controlled through the integer logging_level:

  • level 0 : only critical errors are printed, everything else is suppressed
  • level 1 : only critical errors and warnings are printed
  • level 2 : prints info messages, warnings and critical errors
  • level 3 : (or higher) prints debug messages in addition to all of the above
Parameter Type Description Default value
write_matrices logical if .true. the matrices are written to the datfile .false.
write_eigenfunctions logical if .true. eigenfunctions are calculated and written to the datfile .true.
show_results logical calls the python wrapper after the run is finished and plots the results, requires pylbo_wrapper.py to be in the same directory as the executable. .true.
basename_datfile string the base name of the datfile, this is prepended with the output directory and appended with ".dat" "datfile"
basename_logfile string if not an empty string, saves the eigenvalues to a plain text file with name basename_logfile.log (mainly used for testing) ""
output_folder string the output folder, this is prepended to the datfile name "output"
logging_level int controls the amount of console info, see the note above 2
dry_run logical if .true. forces all eigenvalues to zero and does not call the solver, useful for iterating over the equilibrium implementation .false.

paramlist

This namelist handles constant parameters which are used in the equilibrium prescriptions, and is only read in if use_defaults = .false.. This is meant to be used in parameter studies, for a comprehensive list of all the possible parameters we refer to this page in the Legolas source code documentation. To see which parameters are used in which equilibria, take a look here.