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- 1. Main sections
- 1.1 Section [system]
- 1.2 Section [run]
- 1.3 Section [cosmology]

- 2. Catalog sections

The configuration file for ARES uses the INI file syntax. It is separated into sections among which three are main sections.

- console_output: Holds the prefix filename for all log output files.
- VERBOSE_LEVEL: Set the verbosity level for the console. Files get all outputs.
- N0: Number of grid elements along the X axis.
- N1: Same for Y axis.
- N2: Same for Z axis.
- L0: Comoving length of the X axis
- L1: Same for Y axis
- L2: Same for Z axis
- corner0: Center of the voxel at the corner of the box in -X direction, this should be the smallest X value.
- corner1: Same for Y
- corner2: Same for Z
- NUM_MODES: number of bins to represent the power spectrm
- N_MC: Maximum number of markov chain samples to produce in a single run
- borg_supersampling: Supersampling level of the grid for intermediate calculations
- hades_likelihood: Likelihood to use in HADES run. Can be either one of those values:
- BORG_POISSON: Use poisson likelihood
- BORG_LINEAR: ARES likelihood model. Noise is Gaussian with Variance equal to <math>S \bar{N}</math>. Use power law bias.
- BORG_SH:
- BORG_NB: Negative binomial. Broken power law bias.
- GAUSSIAN_MO_WHITE_BIAS: Gaussian noise model, variance is fitted. Double power law bias

- hades_forward_model: Forward model to use
- LPT: Lagrangian perturbation theory, ModifiedNGP/Quad final projection
- 2LPT: Second order Lagrangian perturbation theory, ModifiedNGP/Quad final projection
- PM: Particle mesh, ModifiedNGP/Quad final projection
- LPT_CIC: Same as LPT, but use CIC for final projection
- 2LPT_CIC: Same as LPT, but use CIC for final projection
- PM_CIC: Same as LPT, but use CIC for final projection
- HADES_LOG: Use Exponential transform (HADES model) for the forward model. Preserved mean density is enforced.

- borg_do_rsd: Do redshift space distortion if set to "true".
- projection_model: Specifies which projection to use for data. No constraints are enforced on the likelihood, but of course they should be matched to the value adopted here.
- number_ngp: it just counts the number of galaxies/objects within a voxel
- luminosity_cic: it weights galaxies by their luminosity and do a CIC projection.

- test_mode: Runs ARES/BORG/HADES in test mode. Data is not used, mock data is generated on the fly.
- seed_cpower: Set to true to seed the power spectrum with the correct one according to the cosmology section. Otherwise it is set to a small fraction of it.
- hades_max_epsilon: Stepsize for the HMC. It is unitless. Good starting point is around 0.01.
- hades_max_timesteps: Maximum number of timesteps for a single HMC sample.
- hades_mixing: Number of samples to compute before writing to disk.
- savePeriodicity: This reduces the number of times the restart files are dumped to the hard drives. This is useful for reducing I/Os, as restart files are heavy. You can set this to a number that is a multiple of the number of mcmc steps. For example, 20 tells ares to dump restart files every 20 mcmc steps.
- mask_precision: Precision to which you want to compute the mask. By default it is "0.01", which is not related to the actual precision (unfortunately not yet). It allows scaling the internal number of evaluation of the selection function. So 0.001 will call it 100 times more. The advice is not to decrease below 0.01.
- furious_seeding: if set to true the core sampler will reseed itself from a system entropy source at each step of the MCMC. That means the MCMC becomes unpredictable and the seed number is discarded.
- simulation: if set to true switches to N-body simulation analysis. Additional cuts are possible depending on masses, spins, etc, of halos.

Likelihoods that use the generic bias framework (currently GAUSSIAN_MO_WHITE_BIAS) supports also the following tags:

- bias_XX_sampler_generic_blocked: if sets to true, it will not sampling the XX parameter of the bias. XX varies depending on the likelihood.

- NCAT: Number of catalogs. This affects the number of "catalog" sections.

- omega_r: Radiation density
- omega_k: Curvature
- omega_m: Total matter density
- omega_b: Baryonic matter density
- omega_q: Quintescence density
- w: Quintescence equation of state
- wprime: Derivative of the equation of state
- n_s: Slope of the power spectrum of scalar fluctuations
- sigma8: Normalisation of powerspectrum at 8 Mpc/h
- h100: Hubble constant in unit of 100 km/s/Mpc

- datafile: Text filename holding the data
- maskdata: Healpix FITS file with the mask
- radial_selection: Type of selection function, can be either "schechter", "file" or "piecewise".
- refbias: true if this catalog is a reference for bias. Bias will not be sampled for it
- bias: Default bias value, also used for mock generation
- nmean: Initial mean galaxy density value, also used for mock generation

- schechter_mstar: Mstar for Schechter function
- schechter_alpha: Power law slope of Schechter function
- schechter_sampling_rate: How many distance points to precompute from Schechter (i.e. 1000)
- schechter_dmax: Maximum distance to precompute Schecter selection functino
- galaxy_bright_apparent_magnitude_cut: Apparent magnitude where data and selection must be truncated, bright end.
- galaxy_faint_apparent_magnitude_cut: Same for faint end.
- galaxy_bright_absolute_magnitude_cut: Absolute magnitude cut in data and selection function, bright end, useful to select different galaxy populations
- galaxy_faint_absolute_magnitude_cut: Similar but faint end
- zmin: Minimum redshift for galaxy sample, galaxies will be truncated
- zmax: Maximum redshift for galaxy sample, galaxies will be truncated

- radial_file: Text file to load the selection from

The file has the following format. Each line starting with a '#' is a comment line, and discarded. The first line is a set of three numbers: 'rmin dr N'. Each line that follows must be a number between 0 and 1 giving the selection function at a distance r = rmin + dr * i, where 'i' is the line number (zero based). Finally 'N' is the number of points in the text file.

Two possibilities are offered for adjusting the catalog and the selection together:

- either you chose not to do anything, and take the whole sample and provided selection. Then you need to specify:
- file_dmin: Minimal distance for selection function and data
- file_dmax: same but maximal distance
- no_cut_catalog: set to false, if you do not set this you will get an error message.

- or you want ares to preprocess the catalog and then you need:
- zmin
- zmax
- galaxy_faint_apparent_magnitude_cut: Same for faint end.
- galaxy_bright_absolute_magnitude_cut: Absolute magnitude cut in data and selection function, bright end, useful to select different galaxy populations
- galaxy_faint_absolute_magnitude_cut: Similar but faint end
- no_cut_catalog: (not necessary, as it defaults to true)