Runtime parameters for rascas

Configuration files are organised in sections that each contains parameters related to a given code module. At runtime, codes from the RASCAS suite will search for the sections they need in the configuration file and parse parameter names. A unique configuration file can thus be used for several codes, and sections which are not needed will be ignored. Sections do not need to be in any particular order. Examples of parameter files can be found in the tests directory.

Note on paths: we recommend defining absolute paths in the parameters.

[RASCAS]

The section [RASCAS] is used to define runtime parameters of the rascas code.

Parameter	Default Value	Fortran type	Description
DomDumpDir	test/	character	Path to the directory where the domain and mesh files are
PhotonICfile	Photon_IC_file.dat	character	Path to the photon packet initial conditions file
fileout	photons_done.dat	character	Path to the standard output file
nbundle	10	integer	Number of photon packets sent by the master to each worker at each message (use a large value (e.g. 10,000) when there are few scatterings per photon packet, and a low value (e.g. 10) for Lyman-alpha)
verbose	.true.	logical	Set verbosity to true or false

[dust]

The section [dust] contains parameters that define the dust modelling. This section is read by module_dust_model.f90.

Parameter	Default Value	Fortran type	Description
albedo	0.32	real	Dust albedo, the value is dust and wavelength dependant. Default 0.32 for Lya, from Li & Draine 2001
g_dust	0.73	real	g parameter of the Henyey-Greenstein phase function for dust scattering. Default 0.73 from Li & Draine 2001
dust_model	SMC	character	Dust extinction law. Could be SMC or LMC

[gas_composition]

The section [gas_composition] is used to define the collection of absorbers that will interact with photons. It is read in module_gas_composition.f90 and uses atomic data from files in the directory atomic_data_dir which are described below.

Parameter	Default Value	Fortran type	Description
nscatterer	–	integer	Number of scatterers in the run
scatterer_names	–	character	List of names of scatterers (e.g., lines)
atomic_data_dir	../ions_parameters/	character	Directory where the atomic data files are located
krome_data_dir	./'	character	Directory where Krome metallic ion density files are located (optional)
f_ion	0.01	real	Ionization factor used in dust density computation
Zref	0.005	real	Reference metallicity (e.g., ~0.005 for SMC, ~0.01 for LMC)
vturb_kms	20.0	real	Constant turbulent velocity across the simulation, in km/s
ignoreDust	.false.	logical	If true, dust is ignored during radiative transfer (but still defined)

The photons may interact with dust and scatterers. Scatterers are defined by their absorption chanel (e.g. HI-1216 refers to the absorption of radiation at H Lyman-alpha). Some absorption channels may lead to multiple de-excitation routes (e.g. fluorescent emission from SiII). This is allowed and described in the atomic data files. There are example files in the ions_parameters directory shipped with the code. The generic format is as follows:

! SiII - 1260.42 line
m_ion          = 28.085d0.      ! mass in atomic mass unit
name_ion       = SiII           ! name of the ion (prefix of line name)
lambda_cm      = 1260.42d-8     ! wavelength in cm
A              = 2.57d9         ! Einstein coefficient A21
f              = 1.22d0.        ! Oscillator strength
n_fluo         = 1              ! number of fluorescent channels (i.e. secondary de-escitation channels)
lambda_fluo_cm = 1265.02d-8     ! wavelengths of these channels 
A_fluo         = 4.73d8         ! Einseint coeff of these channels

HI-Lyman-alpha is a specific case which has the extra following parameters:

isotropic = F        ! controls whether scattering is isotropic or not. 
recoil    = T        ! controls whether the recoil effect is included or not
core_skip = F        ! allows the core-skipping approximation
xcritmax  = 100      ! parameter to moderate the core-skipping approximation
lee_correction = F   ! apply the Lee correction. 

[IdealisedModel]

The section [IdealisedModel] contains parameters that define the idealized models. This section is read by module_idealised_model.f90.

Parameter	Default Value	Fortran type	Description
ColumnDensity_cgs	1d15	real	Column density from the center to the edge of the sphere [cm^-2]
boxsize_cm	1d24	real	Physical size of the simulation box [cm]
Radius_boxUnits	0.48	real	Radius of the sphere in box-size units
Temperature	1d4	real	Gas temperature [K]
TurbulentVelocity_kms	10.0	real	Turbulent velocity dispersion [km/s]

[master]

The section [master] is used to define global runtime parameters and checkpoint/restart options. This section is read by module_master.f90.

Parameter	Default Value	Fortran type	Description
verbose	.false.	logical	Set verbosity flag
restart	.false.	logical	If true, resume run from backup file specified by PhotonBakFile
PhotonBakFile	backup_photons.dat	character	Path to the photon backup file
dt_backup	7200.	real	Time interval between backups [seconds]

[mesh]

The section [mesh] is used to define mesh refinement parameters and settings. It is read in module_mesh.f90. The parameters refine_lmax, refine_err_grad_d, refine_err_grad_v, and refine_dv_over_vth are only used to generate AMR grids for idealised models (i.e. with GenerateAMRmodel). These four parameters are ignored when reading simulation outputs.

Parameter	Default Value	Fortran type	Description
verbose	.true.	logical	Set verbosity to true or false for mesh operations
refine_lmax	8	integer	Maximum level of refinement allowed in the mesh.
refine_err_grad_d	-1.0d0	real	Parameter to control the refinement on density gradients. A cell will be refined if \((\rho_{max}-\rho_{min})/(\rho_{max}+\rho_{min}) >\) refine_err_grad_d, where \(\rho_{max}\) and \(\rho_{min}\) are the max and min values of densities found accross the cell. Setting refine_err_grad_d=0.2 triggers refinement when the density varies by more than 10% accross a cell. If a negative value is passed, this criterion is ignored.
refine_err_grad_v	-1.d0	real	Parameter to control the refinement on velocity gradients. Same as for density above, but now computed on the norm of the velocity field. If a negative value is passed, this criterion is ignored.
refine_dv_over_vth	.false.	logical	Parameter to control the refinement on the velocity field. If set to true, a cell is refined when variations of the norm of the velocity accross the cell are larger than the local thermal velocity.

[mock]

The section [mock] is used to define parameters for the generation of mock observations. This section is read by module_mock.f90.

Parameter	Default Value	Fortran type	Description
nDirections	0	integer	Number of viewing directions for mock observations
mock_parameter_file	—	character	Path to the mock parameter configuration file
mock_outputfilename	—	character	Prefix for output mock files (including absolute path); suffixes .flux, .image, .spectrum, or .cube will be added automatically

The mock parameter configuration file is a text file that contains one block per direction (or pointing). Each block must contain one line per entry as detailed in the table below. Each block of this file is read by the routine read_a_mock_param_set from module_mock.f90.

Line number	description	units	example	comment
1	a normalised vector giving the direction of observation	none	0., 0., 1.
2	the coordinates of the target	code units	0.5, 0.243, 0.12
3	the radius of the circular aperture within which we collect flux	code units	0.01	If the value is 0, no flux is computed. A non-zero value will generate a .flux output.
4	number of pixels, aperture radius, min and max wavelengths	no units, code units, Angstrom, Angstrom	200, 0.01, 1300., 1600.	If the number of pixels is set to zero, no spectrum is computed. Otherwise, a spectrum is computed and written in the .spectrum file.
5	number of pixels on each side of the image, size of the image	no units, code units	200, 0.01	If the number of pixels is zero, no image is computed. Otherwise, an image is computed and written to the .image file.
6	number of pixels in the spectral dimension, number of pixels in the spatial dimensions, min and max wavelengths, side	none, none, Angstrom, Angstrom, code units	50, 100, 1200, 1230, 0.01	If any number of pixels is zero, no cube is computed. Otherwise, a cube is computed and written to the .cube file.

[ramses]

The section [ramses] is used to define RAMSES simulation parameters and RT variable settings. This section is read by module_ramses.f90.

Parameter	Default Value	Fortran type	Description
self_shielding	.true.	logical	If true, reproduce self-shielding approximation made in RAMSES to compute nHI
ramses_rt	.false.	logical	If true, read RAMSES-RT output and compute nHI and T accordingly
read_rt_variables	.false.	logical	If true, read RT variables (e.g. to compute heating terms)
cosmo	.true.	logical	If false, assume idealised simulation
use_proper_time	.false.	logical	If true, use proper time instead of conformal time for cosmo runs
particle_families	.false.	logical	If true, all particles have an extra family field, and the header file is different
verbose	.false.	logical	Display some run-time info on this module
itemp	5	integer	Index of thermal pressure
imetal	6	integer	Index of metallicity
ihii	7	integer	Index of HII fraction
iheii	8	integer	Index of HeII fraction
iheiii	9	integer	Index of HeIII fraction
deut2H_nb_ratio	3.0d-5	real	Ratio between deuterium and hydrogen
recompute_particle_initial_mass	.false.	logical	If true, recompute particle initial mass
tdelay_SN	10.	real	Time delay for supernovae in Myr, only used if recompute_particle_initial_mass is true
recyc_frac	0.8	real	Recycling fraction to correct for mass of stars formed, only used if recompute_particle_initial_mass is true

[uparallel]

The section [uparallel] is used to define parameters for parallel velocity computation methods. This section is read by module_uparallel.f90.

Parameter	Default Value	Fortran type	Description
method	RASCAS	character	Computation method, may be ‘Smith’, ‘Semelin’, or ‘RASCAS’
xForGaussian	8.0	real	Above this value, use a Gaussian to draw u_parallel

[voigt]

The section [voigt] is used to define the numerical approximation to the Voigt function, used at each interaction. This section is read by module_voigt.f90.

Parameter	Default Value	Fortran type	Description
approximation	COLT	character	Could be ‘COLT’, ‘Tasitsiomi’ or ‘Humlicek_w4’

[worker]

The section [worker] is used to define runtime parameters of the workers. This section is read by module_worker.f90.

Parameter	Default Value	Fortran type	Description
verbose	.false.	logical	Set verbosity flag

[RASCAS-serial]

The section [RASCAS-serial] is used to define input/output files and general settings for a serial RASCAS run.

Parameter	Default Value	Fortran type	Description
DomDumpDir	test/	character	Directory where the outputs of CreateDomDump are located
PhotonICFile	Photon_IC_file.dat	character	Path to the file containing the initial photon packets
fileout	photons_done.dat	character	Path to the output file containing processed photons
verbose	.true.	logical	Set verbosity flag

[CreateDomDump]

The section [CreateDomDump] is used to configure the generation of the meshes (or domain dumps) from a simulation output. It is read by the code CreateDomDump.f90.

Parameter	Default Value	Fortran type	Description
DomDumpDir	test/	character	Directory where the outputs of CreateDomDump will be written
repository	./	character	Ramses run directory (where all output_xxxxx dirs are)
snapnum	1	integer	Ramses output number to use
reading_method	fullbox	character	strategy to read ramses data, could be fullbox, hilbert, select_onthefly, or select_onthefly_h
comput_dom_type	sphere	character	Type of the computational domain (e.g. cube, sphere, shell, slab)
comput_dom_pos	(0.5, 0.5, 0.5)	real	Center position of the computational domain [code units]
comput_dom_rsp	0.3	real	Radius of the spherical computational domain [code units]
comput_dom_size	0.3	real	Size of the cubic computational domain [code units]
comput_dom_rin	0.0	real	Inner radius of a shell computational domain [code units]
comput_dom_rout	0.3	real	Outer radius of a shell computational domain [code units]
comput_dom_thickness	0.1	real	Thickness of a slab computational domain [code units]
decomp_dom_type	sphere	character	Type of the decomposition domain(s) (e.g. cube, sphere, shell, slab). Only works with a number of domains, sharing the same type.
decomp_dom_ndomain	1	integer	Number of domains in the decomposition
decomp_dom_xc	0.5	real	x center of domain(s) [code units]. A list of decomp_dom_ndomain positions should be provided, e.g. 0.25, 0.5, 0.75
decomp_dom_yc	0.5	real	y center of domain(s) [code units]
decomp_dom_zc	0.5	real	z center of domain(s) [code units]
decomp_dom_rsp	0.35	real	Radius of the spherical domain(s) [code units]
decomp_dom_size	–	real	Size of the cubic domain(s) [code units]
decomp_dom_rin	–	real	Inner radius of the shell domain(s) [code units]
decomp_dom_rout	–	real	Outer radius of the shell domain(s) [code units]
decomp_dom_thickness	–	real	Thickness of the slab domain(s) [code units]
verbose	.true.	logical	Set verbosity flag

[LyaPhotonsFromGas]

The section [LyaPhotonsFromGas] is used to configure the generation of Lyman-alpha photon packets from gas emission processes. It is read by the code LyaPhotonsFromGas.f90.

Parameter	Default Value	Fortran type	Description
outputfileRec	LyaPhotIC.recLya	character	Path to the output file for recombination photon packets
outputfileCol	LyaPhotIC.colLya	character	Path to the output file for collisional photon packets
repository	./	character	Path to the base repository directory containing simulation data
snapnum	1	integer	Snapshot number to process from the simulation
emission_dom_type	sphere	character	Type of emission domain geometry (e.g., cube, sphere)
emission_dom_pos	5e-01 5e-01 5e-01	real(3)	Position coordinates (x, y, z) of the emission domain center
emission_dom_rsp	0.3	real	Spherical domain radius parameter
emission_dom_rin	0.	real	Inner radius for shell-type emission domains
emission_dom_rout	0.3	real	Outer radius for shell-type emission domains
emission_dom_size	0.3	real	Size parameter of the emission domain
emission_dom_thickness	0.1	real	Thickness parameter for shell-type emission domains
nPhotonPackets	10000	integer	Total number of photon packets to generate
ranseed	-100	integer	Random seed for photon packet generation
doRecombs	.false.	logical	Enable processing of recombination photons
doColls	.true.	logical	Enable processing of collisional photons
tcool_resolution	3.0	real	Temperature resolution factor for cooling calculations
verbose	.true.	logical	Set verbosity to true or false

[HaPhotonsFromGas]

The section [HaPhotonsFromGas] is used to define runtime parameters related to the generation of H-alpha photons from gas emission processes. It is read by the code HaPhotonsFromGas.f90.

Parameter	Default Value	Fortran type	Description
outputfileRec	HaPhotIC.rec	character	Path to file to which recombination photons will be written
outputfileCol	HaPhotIC.col	character	Path to file to which collisional photons will be written
repository	./	character	RAMSES run directory (where all output_xxxxx folders are)
snapnum	1	integer	RAMSES snapshot number to use
emission_dom_type	sphere	character	Type of the emission domain (e.g. cube, sphere, shell, slab)
emission_dom_pos	(0.5, 0.5, 0.5)	real	Center position of the emission domain [code units]
emission_dom_rsp	0.3	real	Radius of the spherical emission domain [code units]
emission_dom_size	0.3	real	Size of the cubic emission domain [code units]
emission_dom_rin	0.0	real	Inner radius of a shell emission domain [code units]
emission_dom_rout	0.3	real	Outer radius of a shell emission domain [code units]
emission_dom_thickness	0.1	real	Thickness of a slab emission domain [code units]
nPhotonPackets	10000	integer	Number of photon packets to generate
ranseed	-100	integer	Random number generator seed for photon sampling
doRecombs	.false.	logical	Enable sampling of emission from recombinations
doColls	.false.	logical	Enable sampling of emission from collisional excitations
tcool_resolution	0.0	real	Cells with dt * tcool_resolution > tcool are excluded from collisional emission
verbose	.true.	logical	Set verbosity flag

[GenerateAMRmodel]

The section [GenerateAMRmodel] is used to configure the generation of the meshes (or domain dumps) for idealised (analytical) models. It is read by the code GenerateAMRmodel.f90.

Parameter	Default Value	Fortran type	Description
DomDumpDir	test/	character	Directory where the outputs of GenerateAMRmodel will be written
comput_dom_type	sphere	character	Type of the computational domain (e.g. cube, sphere, shell, slab)
comput_dom_pos	(0.5, 0.5, 0.5)	real	Center position of the computational domain [code units]
comput_dom_rsp	0.3	real	Radius of the spherical computational domain [code units]
comput_dom_size	0.3	real	Size of the cubic computational domain [code units]
comput_dom_rin	0.0	real	Inner radius of a shell computational domain [code units]
comput_dom_rout	0.3	real	Outer radius of a shell computational domain [code units]
comput_dom_thickness	0.1	real	Thickness of a slab computational domain [code units]
decomp_dom_type	cube	character	Type of the decomposition domain(s) (e.g. cube, sphere, shell, slab). Only works with a number of domains, sharing the same type.
decomp_dom_ndomain	1	integer	Number of domains in the decomposition
decomp_dom_xc	0.5	real	x center of domain(s) [code units]. A list of decomp_dom_ndomain positions should be provided, e.g. 0.25, 0.5, 0.75
decomp_dom_yc	0.5	real	y center of domain(s) [code units]
decomp_dom_zc	0.5	real	z center of domain(s) [code units]
decomp_dom_rsp	–	real	Radius of the spherical domain(s) [code units]
decomp_dom_size	1.	real	Size of the cubic domain(s) [code units]
decomp_dom_rin	–	real	Inner radius of the shell domain(s) [code units]
decomp_dom_rout	–	real	Outer radius of the shell domain(s) [code units]
decomp_dom_thickness	–	real	Thickness of the slab domain(s) [code units]
verbose	.true.	logical	Set verbosity flag

[PhotonsFromStars]

The section [PhotonsFromStars] is used to configure the generation of continuum photon packets from the stellar populations. It is read by the code PhotonsFormStars.f90.

Parameter	Default Value	Fortran type	Description
outputfile	PhotICs.dat	character	Path to the output file for the photon packets
repository	./	character	Path to the base repository directory containing simulation data
snapnum	1	integer	Snapshot number to process from the simulation
star_dom_type	cube	character	Geometry of the domain containing the emitting stars. Could be cube, sphere, shell, or slab
star_dom_pos	5e-01 5e-01 5e-01	real(3)	Position coordinates (x, y, z) of the domain center
star_dom_rsp	0.3	real	Spherical domain radius parameter
star_dom_rin	0.	real	Inner radius for shell-type emission domains
star_dom_rout	0.3	real	Outer radius for shell-type emission domains
star_dom_size	0.3	real	Size parameter of the emission domain
star_dom_thickness	0.1	real	Thickness parameter for shell-type emission domains
spec_type	Mono	character	Spectral shape of the emitting stars. Could be Mono, Gauss, PowLaw, or Table
spec_SSPdir	../libs/SSPlibs/	character	The SSP lib directory
spec_mono_lambda0	1216.	real	Monochromatic emission wavelength [A]
spec_gauss_lambda0	1216.	real	Central wavelength [A] of the Gaussian distribution
spec_gauss_sigma_kms	10.0	real	Line width in velocity [km/s] of the Gaussian distribution
spec_table_lmin_Ang	1120.	real	min wavelength [A] for the sampling of the tabulated spectrum
spec_table_lmax_Ang	1320.	real	max wavelength [A] for the sampling of the tabulated spectrum
spec_powlaw_lmin_Ang	1120.	real	min wavelength [A] for the sampling of a power-law continuum
spec_powlaw_lmax_Ang	1320.	real	max wavelength [A] for the sampling of a power-law continuum
spec_powlaw_Fitlmin_Ang	1100.	real	min wavelength [A] for the fit
spec_powlaw_Fitlmax_Ang	1400.	real	max wavelength [A] for the fit
spec_powlaw _AbsorptionLineClipping	.true.	logical	If true remove absorption lines from fit
nPhotonPackets	1000000	integer	Total number of photon packets to generate
ranseed	-100	integer	Random seed for photon packet generation
verbose	.true.	logical	Set verbosity to true or false

[ExtractSubvol]

The code ExtractSubvol.f90 is a post-processing tool for RAMSES simulations. It is inherited from the code CreateDomDump.f90. The basic idea is to extract from a RAMSES snapshot a subvolume of the simulation using the domain strategy of RASCAS. This cutout is then easy to manipulate with Python. It also uses the rebuilding of the oct-tree structure for the selected cells, allowing the use of neighbors to compute some properties (e.g. velocity dispersion).

Parameter	Default Value	Fortran type	Description
DomDumpDir	test/	character	Directory where the outputs of CreateDomDump will be written
repository	./	character	Ramses run directory (where all output_xxxxx dirs are)
snapnum	1	integer	Ramses output number to use
reading_method	fullbox	character	strategy to read ramses data, could be fullbox, hilbert, select_onthefly, or select_onthefly_h
decomp_dom_type	sphere	character	Type of the decomposition domain (e.g. cube, sphere, shell, slab).
decomp_dom_xc	0.5	real	x center of domain [code units]
decomp_dom_yc	0.5	real	y center of domain [code units]
decomp_dom_zc	0.5	real	z center of domain [code units]
decomp_dom_rsp	0.5	real	Radius of the spherical domain [code units]
decomp_dom_size	0.3	real	Size of the cubic domain [code units]
decomp_dom_rin	0.0	real	Inner radius of the shell domain [code units]
decomp_dom_rout	0.3	real	Outer radius of the shell domain [code units]
decomp_dom_thickness	0.1	real	Thickness of the slab domain [code units]
verbose	.false.	logical	Set verbosity flag
add_stars	.false.	logical	If true add the stellar particles contained in the domain to the cutout.
add_dm	.false.	logical	Same for DM particles. Not implemented yet.

[PhotonsFromSourceModel]

The section [PhotonsFromSourceModel] is used to configure the generation of photon packets from idealised source models. It is read by the code PhotonsFromSourceModel.f90.

Parameter	Default Value	Fortran type	Description
outputfile	ppic.dat	character	Define the path to the output file
source_type	pointlike	character	Can only be point like
source_pos	0.5 0.5 0.5	real	Coordinates of the source (x,y,z), in box units
source_vel	0.0 0.0 0.0	real	Velocity of the source (vx,vy,vz), in cm/s
nPhotonPackets	1000	integer	Number of photon to launch from the source
spec_type	Gauss	character	Could be ‘Mono’ or ‘Gauss’ or ‘PowLaw’ or ‘Table’ or ‘TablePowerLaw’
spec_mono_l0_Ang	1215.67	real	Wavelength of the source in Angstrom, only used if spec_type = Mono
spec_gauss_l0_Ang	1215.67	real	Central wavelength of the gaussian in Angstrom, only used if spec_type = Gauss
spec_gauss_sigma_kms	10.0	real	Width of the gaussian in km/s, only used if spec_type = Gauss
spec_powlaw_lmin_Ang	1120.0	real	min wavelength to sample in Angstrom, only used if spec_type = PowLaw
spec_powlaw_lmax_Ang	1320.0	real	max wavelength to sample in Angstrom, only used if spec_type = PowLaw
spec_powlaw_beta	-2.3	real	Power law index, only used if spec_type = PowLaw
spec_SSPdir	../libs/SSPlibs/	character	Path to the SSP lib directory, only used if spec_type = Table or spec_type = TablePowLaw
spec_table_lmin_Ang	1120.0	real	min wavelength to sample in Angstrom, only used if spec_type = Table
spec_table_lmax_Ang	1320.0	real	max wavelength to sample in Angstrom, only used if spec_type = Table
spec_table_age	10.0	real	Age of the stellar population to use in Myr, only used if spec_type = Table or spec_type = TablePowLaw
spec_table_met	0.02	real	Metallicity of the stellar population to use, only used if spec_type = Table or spec_type = TablePowLaw
spec_table_mass	1.e6	real	Mass of the source in solar mass, only used if spec_type = Table or spec_type = TablePowLaw
spec_tpl_lmin_Ang	1120.0	real	min wavelength to sample in Angstrom, only used if spec_type = TablePowLaw
spec_tpl_lmax_Ang	1320.0	real	max wavelength to sample in Angstrom, only used if spec_type = TablePowLaw
spec_tpl_Fitlmin_Ang	1100.	real	min wavelength to sample for fit, only used if spec_type = TablePowLaw
spec_tpl_Fitlmax_Ang	1500.	real	max wavelength to sample for fit, only used if spec_type = TablePowLaw
spec_tpl_AbsorptionLineClipping	.true.	logical	If true remove absorption lines from fit, only used if spec_type = TablePowLaw
ranseed	1234	integer	Seed for the random generator
verbose	.true.	logical	Set verbosity flag